1. TextbookofBiochemistrywithClinicalCorrelations FourthEdition

2. AbberviationsinBiochemistry A(orAde) adenine ACP acylcarrierprotein ACTH adrenocorticotropichormone acylcoA acylderivativeofCoA ADH antidiuretichormone AdoMet adenosylmethionine Ala alanine ALA aminolevulinicacid AMP adenosinemonophosphate cAMP cyclicAMP Arg arginine Asn asparagine Asp aspartate ATP adenosinetriphosphate ATPase adenosinetriphosphatase BMR basalmetabolicrate BPG D2,3hisphosphoglycerate C(orCyt) cytosine CDP cytidinediphosphate CMP cytidinemonophosphate CTP cytidinetriphosphate CoAorCoASH coenzymeA CoQ coenzymeQ(ubiquinone) cyclicAMP adenosine3 ,5 cyclicmonophosphate cyclicGMP xuanosine3 ,5 cyclicmonophosphate Cys cysteine d 2 deoxyriho DNA deoxyribonucleicacid cDNA complementaryDNA dopa 3,4dihydroxyphenylalanine EcoR1 EcoR1restrictionendonuclease FAD flavinadeninedinucleotide(oxidizedform) FADH2 flavinadeninedinucleotide(reducedform) fMet formylmethionine FMN flavinmononucleotide(oxidizedform) FMNH2 flavinmononucleotide(reducedform) Fp flavoprotein G(orGua) guanine GABA gaminobutyricacid Gal galactose Glc glucose Gln glutamine Glu glutamate Gly glycine GDP guanosinediphosphate GMP guanosinemonophosphate GTP guanosinetriphosphate GSH glutathione Hb hemoglobin HbCO carbonmonoxidehemoglobin HbO2 oxyhemoglobin HDL highdensitylipoprotein HMGCoA bhydroxybmethylglutarylCoA Hyp hydroxyproline IDL intermediatedensitylipoprotein IgG immunoglobulinG Ile isoleucine IP3 inositol1,4,5trisphosphate ITP inosinetriphosphate Km MichaelisMentenconstant kb kilobasepair LDL lowdensitylipoprotein Leu leucine Lys lysine Mb myoglobin MbO2 oxymyoglobin Met methionine MetHb methemoglobin NAD+ nicotinamideadeninedinucleotide(oxidizedform) NADH nicotinamideadeninedinucleotide(reducedform) NADP+ nicotinamideadeninedinucleotidephosphate(oxidizedform) NADPH nicotinamideadeninedinucleotidephosphate(reducedform) NANA Nacetylneuraminicacid PEP phosphoenolpyruvate Phe phenylalanine Pi inorganicorthophosphate PG prostaglandin PPi inorganicpyrophosphate Pro proline PRPP phosphoribosylpyrophosphate Q ubiquinone(CoQ) RNA ribonucleicacid mRNA messengerRNA rRNA ribosomalRNA tRNA transferRNA RNase ribonuclease RQ respiratoryquotient(CO2production/O2consumption) S Svedbergunit SAM Sadenosylmethionine Ser serine SH sulfhydryl T(orThy) thymine TCA Tricarhoxylicacidcycle(Krebscycle) TG triacylglycerol THF tetrahydrofolicacid Thr threonine TPP thiaminepyrophosphate Trp tryptophan TTP thymidinetriphosphate Tyr tyrosine U(orUra) uracil UDP uridinediphosphate UDPgalactose uridinediphosphategalactose UDPglucose uridinediphosphateglucose UMP uridinemonophosphate UTP uridinetriphosphate Val valine VLDL verylowdensitylipoprotein 3. Pageiii TextbookofBiochemistrywithClinicalCorrelations: FourthEdition Editedby ThomasM.Devlin,Ph.D. ProfessorEmeritus DepartmentofBiochemistry MCPHahnemannSchoolofMedicine AlleghenyUniversityoftheHealthSciences Philadelphia,Pennsylvania 4. Pageiv AddressAllInquiriestothePublisher WileyLiss,Inc.,605ThirdAvenue,NewYork,NY101580012 Copyright1997WileyLiss,Inc. PrintedintheUnitedStatesofAmerica. Thistextisprintedonacidfreepaper. Undertheconditionsstatedbelowtheownerofcopyrightforthisbookherebygrantspermissiontouserstomakephotocopyreproductionsofanypartorallofits contentsforpersonalorinternalorganizationaluse,orforpersonalorinternaluseofspecificclients.Thisconsentisgivenontheconditionthatthecopierpaythestated percopyfeethroughtheCopyrightClearanceCenter,Incorporated,27CongressStreet,Salem,MA01970,aslistedinthemostcurrentissueof"Permissionsto Photocopy"(Publisher'sFeelist,distributedbyCCC,Inc.),forcopyingbeyondthatpermittedbysections107or108oftheUSCopyrightLaw.Thisconsentdoes notextendtootherkindsofcopyingforgeneraldistribution,foradvertisingorpromotionalpurposes,forcreatingnewcollectiveworks,orforresale. CoverIllustration:Anartist'sconceptionoftheinitiationoftheDNAtranscriptionmechanismcatalyzedbyRNApolymeraseandinvolvingproteintranscription factors. SubjectEditor:StephanieDiment Design:LauraIerardi SeniorManagingEditor:JohnSollami MarketingManagers:DavidStierandDavidSteltenkamp ManufacturingManager:RickMumma IllustrationCoordinator:BarbaraKennedy IllustrationsandCover:PageTwo ThisbookwassetinITCGaramondLightbyBiCompIncorporated,andwasprintedandboundbyVonHoffmannPress. LibraryofCongressCataloginginPublicationData Textbookofbiochemistry:withclinicalcorrelations/editedby ThomasM.Devlin4thed. p.cm. Includesbibliographicalreferencesandindex. ISBN0471154512 1.Biochemistry.2.Clinicalbiochemistry.I.Devlin,ThomasM. [DNLM:1.Biochemistry.QU4T3551997] QP514.2.T41997971078 612'.015dc21CIP 109876543 5. Pagev To Katie,Matthew,Ryan,andLaura 6. Pagevii Contributors SteliosAktipis,Ph.D. Professor DepartmentofMolecularandCellularBiochemistry StritchSchoolofMedicine LoyolaUniversityofChicago 2160S.FirstAvenue Maywood,IL60153 CarolN.Angstadt,Ph.D. Professor DepartmentofBiomedicalSciences,M.S.#456 AlleghenyUniversityoftheHealthSciences BroadandVineStreets Philadelphia,PA191021192 email:angstadt@allegheny WilliamAwad,JR.,M.D.,Ph.D. Professor DepartmentsofMedicineandofBiochemistry UniversityofMiamiSchoolofMedicine P.O.Box016960 Miami,FL33101 email:wawad@mednet.med.miami.edu JamesBaggott,Ph.D. AssociateProfessor DepartmentofBiochemistry MCPHahnemannSchoolofMedicine AlleghenyUniversityoftheHealthSciences 2900QueenLane Philadelphia,PA19129 email:baggottj@allegheny.edu StephenG.Chaney,Ph.D. Professor DepartmentsofBiochemistryandBiophysicsandofNutrition MaryEllenJonesBuilding UniversityofNorthCarolinaatChapelHillSchoolofMedicineCB#7260 ChapelHill,NC275997260 email:schaney.biochem@mhs.unc.edu MargueriteW.Coomes,Ph.D. AssociateProfessor DepartmentofBiochemistryandMolecularBiology HowardUniversityCollegeofMedicine 520WStreet,N.W. Washington,DC200590001 email:mwcoomes@erols.com JosephG.Cory,Ph.D. ProfessorandChair DepartmentofBiochemistry BrodyMedicalSciencesBuilding EastCarolinaUniversitySchoolofMedicine Greenville,NC278584354 DavidW.Crabb,M.D. Professor DepartmentsofMedicineandofBiochemistryandMolecularBiology EmersonHall317 IndianaUniversitySchoolofMedicine 545BarnhillDrive Indianapolis,IN462025124 email:dcrabb@medicine.dmed.iupi.edu ThomasM.Devlin,Ph.D. ProfessorEmeritus DepartmentofBiochemistry MCPHahnemannSchoolofMedicine AlleghenyUniversityoftheHealthSciences BroadandVineStreets Philadelphia,PA191021192 email:devlint@allegheny.edu JohnE.Donelson,Ph.D. Professor HowardHughesMedicalInstituteandDepartmentofBiochemistry UniversityofIowaCollegeofMedicine 300EcksteinMedicalResearchBuilding IowaCity,IA52242 email:jedonels@vaxa.weeg.viowa.edu 7. Pageviii RobertH.Glew,Ph.D. ProfessorandChair DepartmentofBiochemistry BasicMedicalScienceBuilding,Room249 UniversityofNewMexico SchoolofMedicine 915CaminodeSaludNE Albuquerque,NM87131 email:rglew@medusa.unm.edu DohnG.Glitz,Ph.D. Professor DepartmentofBiologicalChemistry UCLASchoolofMedicine LosAngeles,CA900951737 email:dglitz@biochem.medsch.ucla.edu RobertA.Harris,Ph.D. ShowalterProfessorandChair DepartmentofBiochemistryandMolecularBiology IndianaUniversitySchoolofMedicine 635BarnhillDrive Indianapolis,IN462025122 email:raharris@indyvax.dupui.edu UlrichHopfer,M.D.,Ph.D. Professor DepartmentofPhysiologyandBiophysics CaseWesternReserveUniversity 2109AbingtonRoad Cleveland,OH441064970 email:uxh@po.cwru.edu MichaelN.Liebman,Ph.D. Director,BioinformaticsandGenomics VYSIS,Inc. 3100WoodcreekDrive DownersGrove,IL60515 email:mliebman@vysis.com GeraldLitwack,Ph.D. ProfessorandChair DepartmentofBiochemistryandMolecularPharmacology DeputyDirectorKimmelCancerInstitute JeffersonMedicalCollege ThomasJeffersonUniversity 233South10thStreet Philadelphia,PA19107 email:litwack@lac.jci.tju.edu BettieSueSilerMasters,Ph.D. RobertA.WelchFoundationProfessorinChemistry DepartmentofBiochemistry UniversityofTexasHealthScienceCenteratSanAntonio 7703FloydCurlDrive SanAntonio,TX782847760 email:masters@uthscsa.edu DenisMcGarry,Ph.D. Professor DepartmentsofInternalMedicineandofBiochemistry Bldg.G5,Room210 UniversityofTexasSouthwesternMedicalCenteratDallas 5323HarryHinesBlvd Dallas,TX752359135 email:utsmc.1nparke@mednet.swmed.edu RichardT.Okita,Ph.D. Professor DepartmentofPharmaceuticalScience 105WegnerHall CollegeofPharmacy WashingtonStateUniversity Pullman,WA991646510 email:okitar@mail.wsu.edu MerleS.Olson,Ph.D. ProfessorandChair DepartmentofBiochemistry UniversityofTexasHealthScienceCenter 7703FloydCurlDrive SanAntonio,TX782847760 email:olson@bioc02.uthscsa.edu FrancisJ.Schmidt,Ph.D. Professor DepartmentofBiochemistry M121MedicalSciences UniversityofMissouriColumbia Columbia,MO652120001 email:bcfranks@muccmail.missouri.edu ThomasJ.Schmidt,Ph.D. AssociateProfessor DepartmentofPhysiologyandBiophysics 5610BowenScienceBuilding UniversityofIowa,CollegeofMedicine IowaCity,IA522421109 email:thomasschmidt@uiowa.edu 8. Pageix RichardM.Schultz,Ph.D. ProfessorandChair DepartmentofMolecularandCellularBiochemistry StritchSchoolofMedicine LoyolaUniversityofChicago 2160SouthFirstAvenue Maywood,IL60153 email:rschult@luc.edu NancyB.Schwartz,Ph.D. Professor DepartmentsofPediatricsandofBiochemistryandMolecularBiology UniversityofChicago,MC5058 5841S.MarylandAve. Chicago,IL606371463 email:nschwartz@u.chicago.edu ThomasE.Smith,Ph.D. ProfessorandChair DepartmentofBiochemistryandMolecularBiology CollegeofMedicine HowardUniversity 520WStreet,N.W. Washington,DC200590001 email:tesmith@erols.com GeraldSoslau,Ph.D. Professor DepartmentofBiochemistryandDirector,IMSProgram MCPHahnemannSchoolofMedicine,M.S.344 AlleghenyUniversityoftheHealthSciences BroadandVineStreets Philadelphia,PA191021192 email:soslaug@allegheny.edu J.LyndalYork,Ph.D. Professor DepartmentofBiochemistryandMolecularBiology CollegeofMedicine UniversityofArkansasforMedicalScience 4301W.MarkhamSt. LittleRock,AR722057199 email:jlyork@life.uams.edu 9. Pagexi Foreword Theseareveryexcitingtimesforbiochemistryandespeciallyforthatpartthatpertainstohumanbiologyandhumanmedicine.ThemuchdiscussedHumanGenome Projectislikelytobecompletedveryearlyinthenextmillennium,bythetimemostusersofTextbookofBiochemistryWithClinicalCorrelationshavegraduated. TheHumanGenomeProjectshouldprovideablueprintofthe100,000orsogenesthatthehumangenomeisestimatedtocontainandleadtoanexplosionofamazing proportionsinknowledgeoncomplexphysiologicalprocessesandmultigenicdisorders.Thismappingwillrevealundreamedofinterrelationshipsandelucidatecontrol mechanismsofthefundamentalprocessesofdevelopmentofthehumanorganismandoftheirinteractionswithbothmilieus(theinternalandexternal).Already,one eukaryoticgenome(thatofbrewer'syeast,comprising14millionbasepairsin16chromosomes)wascompletedjustbeforeIsetouttowritethisForeword,while threemicrobialgenomes(thatofMycoplasmagenitalium580,070basepairs,Hemophilusinfluenzae1.83millionbasepairs,andSynechosystisa photosyntheticorganism3.57millionbasepairs)havebeencompletedwithin3to18monthsofisolationoftheirDNA.WorkonthegenomesofMycobacterium tuberculosis(4.5millionbasepairs)andofPlasmodiumfalciparumthemalarialparasite(27millionbasepairsin14chromosomes)isnowbeingundertakenand shouldleadtoknowledgethatcanproducenovelapproachestothetreatmentandcontrolofthesetwoscourgesofhumankind.Thetheoreticalandtechnicalprinciples involvedinthistypeofworkareclearlydescribedinChapters14,15,and18ofTextbookofBiochemistryWithClinicalCorrelations,whichwillensurethat readerswillunderstandandappreciatefuturedevelopmentsinthefield. Discoveriesonthemolecularbasisofhumandiseasearealsobeingreportedatanunprecedentedanddizzyingrate,openingwiderandwiderthewindowtomanyless frequentafflictionsproducedbymutatedgenesaccumulatinginthehumangenepool.Theeraofmolecularmedicinehasalreadyarrived.Sincetheveryfirsteditionof TextbookofBiochemistryWithClinicalCorrelations,thecorrelationshavebeenafeaturethathasmadethebooktrulyunique.Inthisnewedition,thecorrelations arenumerous,succinct,andintegratedwith,butalsoindependentof,thetext.Theynotonlyreflectcurrentprogressbutindicatemorethaneverbeforehow biochemistry,molecularbiology,andhumangeneticshavebecomethefoundationstonesofallareasofmodernmedicine.Thesepreviouslyseparatedisciplineshave becomesointimatelyandinextricablyintertwinedthatlittleknowledgeandunderstandingofonecanoccurwithoutknowledgeandunderstandingofothers.Oneofthe manystrengthsofthisbookisthatclearexamplesoftheconvergenceandintegrationofbiologicaldisciplinescanbefoundintheclinicalcorrelations. InthisfourtheditionofTextbookofBiochemistryWithClinicalCorrelations,thecontributorshaveprovidedanuptodateandlogicalcoverageofbasic biochemistry,molecularbiology,andnormalandabnormalaspectsofphysiologicalchemistry.Thismaterialisappropriateandrelevantformedicalandotherhealth sciencestudents,particularlyasweapproachthethirdmilleniuminthemidstofamazingandpervasiveprogressinmedicalscienceandbiotechnology.Toenhancethe text,acompletelynewseriesofvividillustrationshasbeenadded,whichwillundoubtedlyfurtherthereaders'understandingofthecomplexityofmanyoftheconcepts. Studentsofmedicalandhealthsciencesshouldappreciatethatthetimeandeffortinvestedinlearningthematerialpresentedherewillbeverywellspent.This knowledgewillprovidetheframeworkwithinwhichfurtherdevelopmentswillbeunderstoodandappliedasthereadersbegintocareforthephysicalandmentalwell beingofthoseentrustedtothem.Furthermore,theknowledgederivedfromthisbookwillalsoprovidesatisfyinginsightintotheprocessesthatunderliehumanlifeand theamazingpowerofthehumanmindtoexploreandunderstandit.Asinpreviouseditions,thefourtheditionincludesmanymultiplechoicequestions(andanswers)at theendofeachchapterthatshouldfacilitatethislearningwhileensuringsuccessinprofessionalandotherexaminations. Iamhappyandprivilegedtohavewatchedthegrowthofhumanbiochemistry(becauseofmyteachingandresearchresponsibilities)sincemymedicalstudentdays nearlyhalfacenturyago.Ithasbeenanamazingspectacle,fullofthrillsandexcitingadventuresintoaspectsofhumancellsthatwerepreviouslyshroudedinmystery andignorance.Asmyknowledgehasincreased,sohasmysenseofaweandwonderattheunfoldingbeautyofthismarvelousdisplayofnature'ssecrets. AsthelateAlbertoSolsfrequentlysaid:"TheBiochemistryoftodayistheMedicineoftomorrow."TextbookofBiochemistryWithClinicalCorrelationsillustrates theveracityofthisinsight. FRANKVELLA UNIVERSITYOFSASKATCHEWAN 10. Pagexiii Preface ThepurposesofthefourtheditionoftheTextbookofBiochemistryWithClinicalCorrelationsremainunchangedfromtheearliereditions:topresentaclear discussionofthebiochemistryofmammaliancellstorelatethebiochemicaleventsatthecellularleveltothephysiologicalprocessesoccurringinthewholeanimaland tociteexamplesofdeviantbiochemicalprocessesinhumandisease. Thecontinuedrapidadvancesinknowledge,particularlyduetothetechniquesofmolecularbiology,requiredacriticalreviewandevaluationoftheentirecontentof thepreviousedition.Everychapterhasbeenrevisedandupdated.Significantadditionsofnewmaterial,clarifications,andsomedeletionsweremadethroughout. AminoacidmetabolismwascombinedintoasinglechapterandDNAstructureandfunctionwasdividedintotwochaptersforbettercoverageofthisrapidly expandingfield.Topicsforinclusionwereselectedtocovertheessentialareasofbothbiochemistryandphysiologicalchemistryforupperlevelundergraduate, graduatelevelandespeciallyprofessionalschoolcoursesinbiochemistry.Sincetheapplicationofbiochemistryissoimportanttohumanmedicine,thetexthasan overridingemphasisonthebiochemistryofmammaliancells. Thetextbookiswrittensuchthatanysequenceconsideredmostappropriatebyaninstructorcanbepresented.Itisnotformallydividedintomajorsections,but relatedtopicsaregroupedtogether.Afteranintroductorychapteroncellstructure,Chapters2to5concerntheMajorStructuralComponentsofCells,thatis, proteinsandtheirmanyfunctions,andcellmembranesandtheirmajorroles.Metabolismisdiscussedinthefollowingeightchapters,startingwiththeconservationof energy,thenthesynthesisanddegradationofthemajorcellularcomponents,andconcludingwithachapterontheintegrationofthesepathwaysinhumans.Thenext sectionofsixchapterscoversInformationTransferandItsControl,describingthestructureandsynthesisofthemajorcellularmacromolecules,thatis,DNA, RNA,andprotein.AseparatechapteronBiotechnologyisincludedbecauseinformationfromthisareahashadsuchasignificantimpactonthedevelopmentofour currentstateofbiochemicalknowledge.ThesectionconcludeswithachapterontheRegulationofGeneExpressioninwhichmechanismsinbothprokaryotesand eukaryotesarepresented.ThefourthmajorsectionrepresentsSignalTransductionandAmplificationandincludestwochaptersonhormonesthatemphasizetheir biochemicalfunctionsasmessengersandachapteronMolecularCellBiologydescribesfourmajormammaliansignaltransducingsystems.Thetextbookconcludes withsixchaptersontopicsthatcomprisePhysiologicalChemistry,includingcytochromeP450enzymesandxenobioticmetabolism,ironandhememetabolism,gas transportandpHregulation,digestionandabsorption,andhumannutrition. Amajoradditionfrompreviouseditionsistheextensiveuseofcolorintheillustrationsasameanstoemphasizeimportantpoints.Allfigureswerereviewedandnew drawingswerepreparedtoillustratethenarrativediscussion.Inmanycasestheadage''Apictureisworthathousandwords"isappropriateandthereaderis encouragedtostudytheillustrationsbecausetheyaremeanttoilluminateoftenconfusingaspectsofatopic. IneachchaptertherelevancyofthetopictohumanlifeprocessesarepresentedinClinicalCorrelations,whichdescribetheaberrantbiochemistryofdiseasestates. Anumberofnewcorrelationshavebeenincluded.Thecorrelationsarenotintendedtoreviewallofthemajordiseasesbutrathertociteexamplesofdisease processeswherethebiochemicalimplicationsarewellestablished.Inaddition,wespecificallyavoidedpresentingclinicalcasereportsbecauseitwasconsideredmore significanttodealwiththegeneralclinicalcondition.Referencesareincludedtofacilitateexplorationofthetopicinmoredetail.Insomecasessimilarclinicalproblems arepresentedindifferentchapters,buteachfromadifferentperspective.Allpertinentbiochemicalinformationispresentedinthemaintext,andanunderstandingof thematerialdoesnotrequireareadingofthecorrelations.Inafewcases,clinicaldiscussionsarepartoftheprincipaltextbecauseofthecloserelationshipofsome topicstomedicalconditions. EachchapterconcludeswithasetofQuestionsandAnswersthemultiplechoiceformatwasretainedasbeingvaluabletostudentsforselfassessmentoftheir knowledge.Thequestiontypewaslimitedtothetypesnowoccurringinnationalexaminations.Allquestionswerereviewedandmanynewonesadded.Thequestions coverarangeoftopicsineachchapter,andeachhasanannotatedanswer,withreferencestothepageinthetextbookcoveringthecontentofthequestion. Theappendix,ReviewofOrganicChemistry,isdesignedasareadyreferenceforthenomenclatureandstructuresoforganicmoleculesencounteredin biochemistryandisnotintendedasacomprehensivereviewoforganicchemistry.ThematerialispresentedintheAppendixratherthanatthebeginningofthose chaptersdealingwiththemetabolismofeachclassoforganicmolecules.Thereadermightfindit 11. Pagexiv valuabletobecomefamiliarwiththecontentandthenusetheAppendixasareadyreferencewhenreadingrelatedsectionsinthemaintext. Westillbelievethatamulticontributortextbookisthebestapproachtoachieveanaccurateandcurrentpresentationofbiochemistry.Eachauthorisinvolvedactively inteachingbiochemistryinamedicalorgraduateschoolandhasanactiveresearchinterestinthefieldinwhichheorshehaswritten.Thus,eachhastheperspectiveof theclassroominstructor,withtheexperiencetoselectthetopicsanddeterminetheemphasisrequiredforstudentsinacourseofbiochemistry.Everycontributor, however,bringstothebookanindividualapproach,leadingtosomedifferencesinpresentation.However,everychapterwascriticallyeditedandrevisedinorderto haveaconsistentwritingstyleandtoeliminaterepetitionsandredundancies.Alimitedrepetitionofsometopicsindifferentchapterswaspermittedwhenitwas consideredthattherepetitionwouldfacilitatethelearningprocess. Theindividualcontributorswererequestedtopreparetheirchaptersforateachingbook.Thebookisnotintendedasacompendiumofbiochemicalfactsorareview ofthecurrentliterature,buteachchaptercontainssufficientdetailonthesubjecttomakeitusefulasaresource.Eachcontributorwasrequestednottorefertospecific researchersourapologiestothosemanybiochemistswhorightfullyshouldbeacknowledgedfortheiroutstandingresearchcontributionstothefieldofbiochemistry. EachchaptercontainsaBibliographythatcanbeusedasanentrypointtotheresearchliterature. Inanyprojectonepersonmustaccepttheresponsibilityforthefinalproduct.Thedecisionsconcerningtheselectionoftopicsandformat,reviewingthedrafts,and responsibilityforthefinalcheckingofthebookwereentirelymine.Iwelcomecomments,criticisms,andsuggestionsfromthestudents,faculty,andprofessionalswho usethistextbook.Itisourhopethatthisworkwillbeofvaluetothoseembarkingontheexcitingexperienceoflearningbiochemistryforthefirsttimeandtothosewho arereturningtoatopicinwhichtheinformationisexpandingsorapidly. THOMASM.DEVLIN 12. Pagexv Acknowledgments Withouttheencouragementandparticipationofmanypeople,thisprojectwouldneverhavebeenaccomplished.Mypersonalandverydeepappreciationgoesto eachofthecontributorsforacceptingthechallengeofpreparingthechapters,forsharingtheirideasandmakingrecommendationstoimprovethebook,foraccepting soreadilysuggestionstomodifytheircontributions,andforcooperatingthroughouttheperiodofpreparation.ToeachIextendmysincerestthanksforajobwell done. Thecontributorsreceivedthesupportofassociatesandstudentsinthepreparationoftheirchapters,and,forfearofomittingsomeone,itwasdecidednotto acknowledgeindividualsbyname.Toeveryonewhogavetimeunselfishlyandsharedintheobjectiveandcriticalevaluationofthetext,weextendasincerethankyou. Inaddition,everycontributorhasbeeninfluencedbyformerteachersandcolleagues,variousreferenceresources,and,ofcourse,theresearchliteratureof biochemistrywearedeeplyindebtedtothesemanysourcesofinspiration. IamparticularlyindebtedtoDr.FrankVella,ProfessorofBiochemistryattheUniversityofSaskatchewan,Canada,whoassistedmeineditingthetext.Dr.Vellaisa distinguishedbiochemistwhohasmadeamajorpersonalefforttoimprovetheteachingofbiochemistrythroughouttheworld.Hereadeverychapterindraftformand madesignificantsuggestionsforclarifyingandimprovingthepresentation.Dr.VellaalsohonoredmebywritingtheForewordtothefourtheditionofthistextbook.I extendtohimmydeepestappreciationandthanksforhisparticipationandfriendship. Averyspecialthankstotwofriendsandcolleagueswhoagainhavebeenofimmeasurablevaluetomeduringthepreparationofthisedition:MygratitudegoestoDr. JamesBaggott,whopatientlyallowedmetousehimasasoundingboardforideasandwhounselfishlysharedwithmehissuggestionsandcriticismsofthetext,andto Dr.CarolAngstadt,whoreviewedmanyofthechaptersandgavemevaluablesuggestions.ToeachIextendmydeepestgratitude. IextendmysincerestappreciationandthankstothemembersofthestaffoftheSTMDivisionofJohnWiley&Sonswhoparticipatedinthepreparationofthis edition.SpecialrecognitionandthanksgotoDr.BrianCrawford,VicePresidentandGeneralManagerofLifeSciencesandMedicine,whogavehisunqualified supporttothepreparationofthefourthedition.IamindebtedtoJoeIngram,Publisher,LifeSciences,whoconscientiouslyguidedtheplanningofthisedition.Iam veryindebtedtoDr.StephanieDiment,AssociateEditor,foralwaysbeingavailabletoanswerquestionsandtomakevaluablesuggestions,andwhohaspatientlykept meontrack.Shehasbeenaconstantsupportthankyou.MydeepestappreciationisextendedtoJohnSollami,SeniorManagingEditor,whowithconstantgood humormeticulouslyoversawtheproduction.Hekepttheflowofactivitiesreasonable,listenedpatientlytomysuggestionsandconcerns,andkeptusonschedule.It hasbeenarealpleasuretoworkwithareallyknowledgeableandconscientiousprofessionalandtohimIextendaveryspecialthanks.IextendtoLouisePage,New MediaEditor,mydeepestappreciationforherskillfulorganizationoftheCDcontainingthefiguresfromthetextbook.CreditforthedesignofthebookgoestoLaura Ierardi,towhomIextendmyappreciation.MythankstoChristinaDellaBartolomea,copyeditor,andMariaCoughlin,indexer,bothofwhomdidanexcellentjob.A significantimprovementinthiseditionistheadditionofmanyoriginalillustrations.MymostheartfeltthanksgotoDeanGonzalez.STMIllustrationManager,and BarbaraKennedy,IllustrationSupervisor,atWiley,whohandledthedetailsandflowofillustrations.AspecialrecognitionisextendedtoDr.LisaGardner,Production ManagerandEditorofPageTwo,andherstaffwhotransformedtheroughdrawingsofthecontributorsintomeaningfulillustrations.Nobookissuccessfulwithoutthe activitiesofaMarketingDepartmentspecialthanksareduetoReedElfenbein,VicePresident,MarketingandSales,DavidStier,SeniorMarketingManager,David Steltenkamp,AssociateMarketingManager,andtheircolleaguesatWileyfortheirnewideasandefforts. Finally,averyspecialthankstomyloving,supportive,andconsideratewife,Marjorie,whohadtheforesighttoencouragemetoundertakethisproject,whoagain supportedmeduringthedaysofintensivework,andwhoagaincreatedanenvironmentinwhichIcoulddevotethemanyhoursrequiredforthepreparationofthis textbook.Tohermydeepestappreciation. THOMASM.DEVLIN 13. Pagexvii ContentsinBrief 1 EukaryoticCellStructure 1 2 ProteinsI:CompositionandStructure 23 3 ProteinsII:StructureFunctionRelationshipsinProteinFamilies 87 4 Enzymes:Classification,Kinetics,andControl 127 5 BiologicalMembranes:StructureandMembraneTransport 179 6 BioenergeticsandOxidativeMetabolism 217 7 CarbohydrateMetabolismI:MajorMetabolicPathwaysandtheirControl 267 8 CarbohydrateMetabolismII:SpecialPathways 335 9 LipidMetabolismI:UtilizationandStorageofEnergyinLipidForm 361 10 LipidMetabolismII:PathwaysofMetabolismofSpecialLipids 395 11 AminoAcidMetabolism 445 12 PurineandPyrimidineNucleotideMetabolism 489 13 MetabolicInterrelationships 525 14 DNAI:StructureandConformation 563 15 DNAII:Repair,Synthesis,andRecombination 621 16 RNA:Structure,Transcription,andProcessing 677 17 ProteinSynthesis:TranslationandPosttranslationalModifications 713 18 RecombinantDNAandBiotechnology 757 19 RegulationofGeneExpression 799 20 BiochemistryofHormonesI:PolypeptideHormones 839 21 BiochemistryofHormonesII:SteroidHormones 893 22 MolecularCellBiology 919 23 Biotransformations:TheCytochromesP450 981 24 IronandHemeMetabolism 1001 25 GasTransportandpHRegulation 1025 26 DigestionandAbsorptionofBasicNutritionalConstituents 1055 27 PrinciplesofNutritionI:Macronutrients 1087 28 PrinciplesofNutritionII:Micronutrients 1107 Appendix ReviewofOrganicChemistry 1137 Index 1149 14. Pagexix Contents ThomasM.Devlin 1 EukaryoticCellStructure 1 1.1Overview:CellsandCellularCompartments 2 1.2CellularEnvironment:WaterandSolutes 4 1.3OrganizationandCompositionofEukaryoticCells 12 1.4FunctionalRoleofSubcellularOrganellesandMembraneSystems 15 ClinicalCorrelations 1.1BloodBicarbonateConcentrationinMetabolicAcidosis 12 1.2MitochondrialDiseases:Luft'sDisease 16 1.3LysosomalEnzymesandGout 18 1.4LysosomalAcidLipaseDeficiency 19 1.5ZellwegerSyndromeandtheAbsenceofFunctionalPeroxisomes 20 RichardM.SchultzandMichaelN.Liebman 2 ProteinsI:CompositionandStructure 23 2.1FunctionalRolesofProteinsinHumans 24 2.2AminoAcidCompositionofProteins 25 2.3ChargeandChemicalPropertiesofAminoAcidsandProteins 30 2.4PrimaryStructureofProteins 39 2.5HigherLevelsofProteinOrganization 42 2.6OtherTypesofProteins 49 2.7FoldingofProteinsfromRandomizedtoUniqueStructures:Protein Stability 62 2.8DynamicAspectsofProteinStructure 68 2.9MethodsforCharacterization,Purification,andStudyofProtein StructureandOrganization 69 ClinicalCorrelations 2.1PlasmaProteinsinDiagnosisofDisease 37 2.2DifferencesinPrimaryStructureofInsulinsUsedinTreatmentof DiabetesMellitus 41 2.3ANonconservativeMutationOccursinSickleCellAnemia 42 2.4SymptomsofDiseasesofAbnormalCollagenSynthesis 50 2.5Hyperlipidemias 56 2.6Hypolipoproteinemias 59 2.7GlycosylatedHemoglobin,HbA1c 62 2.8UseofAminoAcidAnalysisinDiagnosisofDisease 74 RichardM.SchultzandMichaelN.Liebman 3 ProteinsII:StructureFunctionRelationshipsinProteinFamilies 87 3.1Overview 88 3.2AntibodyMolecules:TheImmunoglobulinSuperfamily 88 3.3ProteinswithaCommonCatalyticMechanism:SerineProteases 97 3.4DNABindingProteins 108 3.5HemoglobinandMyoglobin 114 ClinicalCorrelations 3.1TheComplementProteins 91 3.2FunctionsofDifferentAntibodyClasses 92 3.3Immunization 92 3.4FibrinFormationinaMyocardialInfarctandtheActionof RecombinantTissuePlasminogenActivator(rtPA) 98 3.5InvolvementofSerineProteasesinTumorCellMetastasis 99 J.LyndalYork 4 Enzymes:Classification,KineticsandControl 127 4.1GeneralConcepts 128 4.2ClassificationofEnzymes 129 4.3Kinetics 133 4.4Coenzymes:StructureandFunction 142 4.5InhibitionofEnzymes 147 4.6AllostericControlofEnzymeActivity 151 4.7EnzymeSpecificity:TheActiveSite 155 4.8MechanismofCatalysis 159 4.9ClinicalApplicationsofEnzymes 166 4.10RegulationofEnzymeActivity 174 ClinicalCorrelations 4.1ACaseofGoutDemonstratesTwoPhasesintheMechanismof EnzymeAction 138 15. Pagexx 4.2ThePhysiologicalEffectofChangesinEnzymeKmValues 139 4.3MutationofaCoenzymeBindingSiteResultsinClinicalDisease 142 4.4ACaseofGoutDemonstratestheDifferencebetweenanAllosteric andSubstrateBindingSite 152 4.5ThermalLabilityofGlucose6PhosphateDehydrogenaseResultsin HemolyticAnemia 166 4.6AlcoholDehydrogenaseIsoenzymeswithDifferentpHOptima 167 4.7IdentificationandTreatmentofanEnzymeDeficiency 169 4.8AmbiguityintheAssayofMutatedEnzymes 169 ThomasM.Devlin 5 BiologicalMembranes:StructureandMembraneTransport 179 5.1Overview 180 5.2ChemicalCompositionofMembranes 180 5.3MicellesandLiposomes 187 5.4StructureofBiologicalMembranes 189 5.5MovementofMoleculesthroughMembranes 196 5.6ChannelsandPores 201 5.7PassiveMediatedTransportSystems 204 5.8ActiveMediatedTransportSystems 206 5.9Ionophores 211 ClinicalCorrelations 5.1LiposomesAsCarriersofDrugsandEnzymes 189 5.2AbnormalitiesofCellMembraneFluidityinDiseaseStates 195 5.3CysticFibrosisandtheCl Channel 202 5.4DiseasesDuetoLossofMembraneTransportSystems 212 MerleS.Olson 6 BioenergeticsandOxidativeMetabolism 217 6.1EnergyProducingandEnergyUtilizingSystems 218 6.2ThermodynamicRelationshipsandEnergyRichComponents 220 6.3SourcesandFatesofAcetylCoenzymeA 226 6.4TheTricarboxylicAcidCycle 231 6.5StructureandCompartmentationbyMitochondrialMembranes 238 6.6ElectronTransfer 246 6.7OxidativePhosphorylation 261 ClinicalCorrelations 6.1PyruvateDehydrogenaseDeficiency 233 6.2FumaraseDeficiency 237 6.3MitochondrialMyopathies 247 6.4SubacuteNecrotizingEncephalomyelopathy 258 6.5CyanidePoisoning 259 6.6HypoxicInjury 261 RobertA.Harris 7 CarbohydrateMetabolismI:MajorMetabolicPathwaysandtheirControl 267 7.1Overview 268 7.2Glycolysis 269 7.3TheGlycolyticPathway 272 7.4RegulationoftheGlycolyticPathway 283 7.5Gluconeogenesis 299 7.6GlycogenolysisandGlycogenesis 312 ClinicalCorrelations 7.1AlcoholandBarbiturates 281 7.2ArsenicPoisoning 283 7.3FructoseIntolerance 285 7.4DiabetesMellitus 287 7.5LacticAcidosis 291 7.6PickledPigsandMalignantHyperthermia 291 7.7AnginaPectorisandMyocardialInfarction 292 7.8PyruvateKinaseDeficiencyandHemolyticAnemia 299 7.9HypoglycemiaandPrematureInfants 300 7.10HypoglycemiaandAlcoholIntoxication 312 7.11GlycogenStorageDiseases 317 NancyB.Schwartz 8 CarbohydrateMetabolismII:SpecialPathways 335 8.1Overview 336 8.2PentosePhosphatePathway 336 8.3SugarInterconversionsandNucleotideSugarFormation 341 8.4BiosynthesisofComplexCarbohydrates 346 8.5Glycoproteins 348 8.6Proteoglycans 351 ClinicalCorrelations 8.1Glucose6PhosphateDehydrogenase:GeneticDeficiencyor PresenceofGeneticVariantsinErythrocytes 338 8.2EssentialFructosuriaandFructoseIntolerance:Deficiencyof FructokinaseandFructose1PhosphateAldolase 342 8.3Galactosemia:InabilitytoTransformGalactoseintoGlucose 343 8.4Pentosuria:DeficiencyofXylitolDehydrogenase 345 8.5GlucuronicAcid:PhysiologicalSignificanceofGlucuronide Formation 346 8.6BloodGroupSubstances 348 8.7Aspartylglycosylaminuria:Absenceof4LAspartylglycosamine Amidohydrolase 349 8.8HeparinIsanAnticoagulant 350 8.9Mucopolysaccharidoses 352 16. Pagexxi J.DenisMcGarry 9 LipidMetabolismI:UtilizationandStorageofEnergyinLipidForm 361 9.1Overview 362 9.2ChemicalNatureofFattyAcidsandAcylglycerols 363 9.3SourcesofFattyAcids 365 9.4StorageofFattyAcidsAsTriacylglycerols 375 9.5MethodsofInterorganTransportofFattyAcidsandtheirPrimary Products 378 9.6UtilizationofFattyAcidsforEnergyProduction 381 ClinicalCorrelations 9.1Obesity 378 9.2LeptinandObesity 378 9.3GeneticAbnormalitiesinLipidEnergyTransport 380 9.4GeneticDeficienciesinCarnitineTransportorCarnitine Palmitoyltransferase 384 9.5GeneticDeficienciesintheAcylCoADehydrogenases 385 9.6Refsum'sDisease 387 9.7DiabeticKetoacidosis 390 RobertH.Glew 10 LipidMetabolismII:PathwaysofMetabolismofSpecialLipids 395 10.1Overview 396 10.2Phospholipids 397 10.3Cholesterol 409 10.4Sphingolipids 420 10.5ProstaglandinsandThromboxanes 431 10.6LipoxygenaseandOxyEicosatetraenoicAcids 436 ClinicalCorrelations 10.1RespiratoryDistressSyndrome 400 10.2TreatmentofHypercholesterolemia 416 10.3Atherosclerosis 417 10.4DiagnosisofGaucher'sDiseaseinanAdult 430 MargueriteW.Coomes 11 AminoAcidMetabolism 445 11.1Overview 446 11.2IncorporationofNitrogenintoAminoAcids 447 11.3TransportofNitrogentoLiverandKidney 452 11.4UreaCycle 453 11.5SynthesisandDegradationofIndividualAminoAcids 456 ClinicalCorrelations 11.1CarbamoylPhosphateSynthetaseandNAcetylglutamate SynthetaseDeficiencies 456 11.2DeficienciesofUreaCycleEnzymes 457 11.3NonketoticHyperglycinemia 461 11.4FolicAcidDeficiency 463 11.5Phenylketonuria 465 11.6DisordersofTyrosineMetabolism 467 11.7Parkinson'sDisease 467 11.8HyperhomocysteinemiaandAtherogenesis 471 11.9OtherDiseasesofSulfurAminoAcids 471 11.10DiseasesofMetabolismofBranchedChainAminoAcids 479 11.11DiseasesofPropionateandMethylmalonateMetabolism 480 11.12DiseasesInvolvingLysineandOrnithine 481 11.13Histidinemia 482 11.14DiseasesofFolateMetabolism 483 JosephG.Cory 12 PurineandPyrimidineNucleotideMetabolism 489 12.1Overview 490 12.2MetabolicFunctionsofNucleotides 490 12.3ChemistryofNucleotides 492 12.4MetabolismofPurineNucleotides 493 12.5MetabolismofPyrimidineNucleotides 503 12.6DeoxyribonucleotideFormation 507 12.7NucleosideandNucleotideKinases 511 12.8NucleotideMetabolizingEnzymesAsaFunctionoftheCellCycleand RateofCellDivision 511 12.9NucleotideCoenzymeSynthesis 514 12.10SynthesisandUtilizationof5Phosphoribosyl1Pyrophosphate 516 12.11CompoundsthatInterferewithCellularPurineandPyrimidine NucleotideMetabolism:ChemotherapeuticAgents 517 ClinicalCorrelations 12.1Gout 498 12.2LeschNyhanSyndrome 499 12.3ImmunodeficiencyDiseasesAssociatedwithDefectsinPurine NucleosideDegradation 503 12.4HereditaryOroticAciduria 505 RobertA.HarrisandDavidW.Crabb 13 MetabolicInterrelationships 525 13.1Overview 526 13.2StarveFeedCycle 528 13.3MechanismsInvolvedinSwitchingtheMetabolismofLiverbetweenthe WellFedStateandtheStarvedState 539 13.4MetabolicInterrelationshipsofTissuesinVariousNutritionaland HormonalStates 547 17. Pagexxii ClinicalCorrelations 13.1Obesity 526 13.2ProteinMalnutrition 527 13.3Starvation 527 13.4Reye'sSyndrome 533 13.5Hyperglycemic,HyperosmolarComa 537 13.6HyperglycemiaandProteinGlycation 538 13.7NoninsulinDependentDiabetesMellitus 549 13.8InsulinDependentDiabetesMellitus 550 13.9ComplicationsofDiabetesandthePolyolPathway 551 13.10CancerCachexia 553 SteliosAktipis 14 DNAI:StructureandConformation 563 14.1Overview 564 14.2StructureofDNA 565 14.3TypesofDNAStructure 584 14.4DNAStructureandFunction 609 ClinicalCorrelations 14.1DNAVaccines 565 14.2DiagnosticUseofProbesinMedicine 583 14.3TopoisomerasesinTreatmentofCancer 594 14.4HereditaryPersistenceofFetalHemoglobin 600 14.5TherapeuticPotentialofTriplexDNAFormation 600 14.6ExpansionofDNATripleRepeatsandHumanDisease 602 14.7MutationsofMitochondrialDNA:AgingandDegenerative Diseases 617 SteliosAktipis 15 DNAII:Repair,Synthesis,andRecombination 621 15.1Overview 622 15.2FormationofthePhosphodiesterBondinVivo 622 15.3MutationandRepairofDNA 627 15.4DNAReplication 642 15.5DNARecombination 661 15.6SequencingofNucleotidesinDNA 671 ClinicalCorrelations 15.1MutationsandtheEtiologyofCancer 633 15.2DefectsinNucleotideExcisionRepairandHereditaryDiseases 638 15.3DNALigaseActivityandBloomSyndrome 639 15.4DNARepairandChemotherapy 639 15.5MismatchDNARepairandCancer 641 15.6TelomeraseActivityinCancerandAging 658 15.7InhibitorsofReverseTranscriptaseinTreatmentofAIDS 661 15.8ImmunoglobulinGenesAreAssembledbyRecombination 663 15.9TransposonsandDevelopmentofAntibioticResistance 670 15.10DNAAmplificationandDevelopmentofDrugResistance 671 15.11NucleotideSequenceoftheHumanGenome 672 FrancisJ.Schmidt 16 RNA:Structure,Transcription,andProcessing 677 16.1Overview 678 16.2StructureofRNA 679 16.3TypesofRNA 681 16.4MechanismsofTranscription 689 16.5PosttranscriptionalProcessing 699 16.6NucleasesandRNATurnover 708 ClinicalCorrelations 16.1StaphylococcalResistancetoErythromycin 683 16.2AntibioticsandToxinsthatTargetRNAPolymerase 692 16.3FragileXSyndrome:AChromatinDisease? 697 16.4InvolvementofTranscriptionalFactorsinCarcinogenesis 701 16.5ThalassemiaDuetoDefectsinMessengerRNASynthesis 705 16.6AutoimmunityinConnectiveTissueDisease 706 DohnGlitz 17 ProteinSynthesis:TranslationandPosttranslationalModifications 713 17.1Overview 714 17.2ComponentsoftheTranslationalApparatus 714 17.3ProteinBiosynthesis 724 17.4ProteinMaturation:Modification,Secretion,andTargeting 735 17.5OrganelleTargetingandBiogenesis 739 17.6FurtherPosttranslationalProteinModifications 743 17.7RegulationofTranslation 748 17.8ProteinDegradationandTurnover 750 ClinicalCorrelations 17.1MissenseMutation:Hemoglobin 721 17.2DisordersofTerminatorCodons 722 17.3Thalassemia 722 17.4MutationinMitochondrialRibosomalRNAResultsinAntibiotic InducedDeafness 734 17.5ICellDisease 740 17.6FamilialHyperproinsulinemia 743 17.7AbsenceofPosttranslationalModification:MultipleSulfatase Deficiency 746 17.8DefectsinCollagenSynthesis 749 18. Pagexxiii 17.9DeletionofaCodon,IncorrectPosttranslationalModification,and PrematureProteinDegradation:CysticFibrosis 752 GeraldSoslau 18 RecombinantDNAandBiotechnology 757 18.1Overview 758 18.2PolymeraseChainReaction 759 18.3RestrictionEndonucleaseandRestrictionMaps 760 18.4DNASequencing 762 18.5RecombinantDNAandCloning 765 18.6SelectionofSpecificClonedDNAinLibraries 770 18.7TechniquesforDetectionandIdentificationofNucleicAcids 773 18.8ComplementaryDNAandComplementaryDNALibraries 777 18.9Bacteriophage,Cosmid,andYeastCloningVectors 778 18.10TechniquestofurtherAnalyzeLongStretchesofDNA 781 18.11ExpressionVectorsandFusionProteins 783 18.12ExpressionVectorsinEukaryoticCells 784 18.13SiteDirectedMutagenesis 786 18.14ApplicationsofRecombinantDNATechnologies 790 18.15ConcludingRemarks 795 ClinicalCorrelations 18.1PolymeraseChainReactionandScreeningforHuman ImmunodeficiencyVirus 760 18.2RestrictionMappingandEvolution 762 18.3DirectSequencingofDNAforDiagnosisofGeneticDisorders 766 18.4MultiplexPCRAnalysisofHGPRTaseGeneDefectsinLesch NyhanSyndrome 770 18.5RestrictionFragmentLengthPolymorphismsDeterminetheClonal OriginofTumors 776 18.6SiteDirectedMutagenesisofHSVIgD 789 18.7NormalGenesCanBeIntroducedintoCellswithDefectiveGenes inGeneTherapy 793 18.8TransgenicAnimalModels 795 JohnE.Donelson 19 RegulationofGeneExpression 799 19.1Overview 800 19.2UnitofTranscriptioninBacteria:TheOperon 800 19.3LactoseOperonofE.Coli 802 19.4TryptophanOperonofE.Coli 807 19.5OtherBacterialOperons 813 19.6BacterialTransposons 816 19.7InversionofGenesinSalmonella 818 19.8OrganizationofGenesinMammalianDNA 820 19.9RepetitiveDNASequencesinEukaryotes 822 19.10GenesforGlobinProteins 824 19.11GenesforHumanGrowthHormoneLikeProteins 829 19.12MitochondrialGenes 830 19.13BacterialExpressionofForeignGenes 832 19.14IntroductionofRatGrowthHormoneGeneintoMice 835 ClinicalCorrelations 19.1TransmissibleMultipleDrugResistances 816 19.2Duchenne/BeckerMuscularDystrophyandtheDystrophinGene 822 19.3Huntington'sDiseaseandTrinucleotideRepeatExpansions 823 19.4PrenatalDiagnosisofSickleCellAnemia 828 19.5PrenatalDiagnosisofThalassemia 829 19.6Leber'sHereditaryOpticNeuropathy(LHON) 831 GeraldLitwackandThomasJ.Schmidt 20 BiochemistryofHormonesI:PolypeptideHormones 839 20.1Overview 840 20.2HormonesandtheHormonalCascadeSystem 841 20.3MajorPolypeptideHormonesandtheirActions 846 20.4GenesandFormationofPolypeptideHormones 849 20.5SynthesisofAminoAcidDerivedHormones 853 20.6InactivationandDegradationofHormones 857 20.7CellRegulationandHormoneSecretion 859 20.8CyclicHormonalCascadeSystems 866 20.9HormoneReceptorInteractions 871 20.10StructureofReceptors:bAdrenergicReceptor 875 20.11InternalizationofReceptors 876 20.12IntracellularAction:ProteinKinases 878 20.13OncogenesandReceptorFunctions 888 ClinicalCorrelations 20.1TestingActivityoftheAnteriorPituitary 844 20.2Hypopituitarism 846 20.3LithiumTreatmentofManicDepressiveIllness:The PhosphatidylinositolCycle 863 GeraldLitwackandThomasJ.Schmidt 21 BiochemistryofHormonesII:SteroidHormones 893 21.1Overview 894 21.2StructuresofSteroidHormones 894 21.3BiosynthesisofSteroidHormones 896 21.4MetabolicInactivationofSteroidHormones 901 21.5CellCellCommunicationandControlofSynthesisandReleaseof SteroidHormones 901 19. Pagexxiv 21.6TransportofSteroidHormonesinBlood 908 21.7SteroidHormoneReceptors 909 21.8ReceptorActivation:UpregulationandDownregulation 914 21.9ASpecificExampleofSteroidHormoneActionatCellLevel: ProgrammedDeath 915 ClinicalCorrelations 21.1OralContraception 907 21.2ApparentMineralocorticoidExcessSyndrome 911 21.3ProgrammedCellDeathintheOvarianCycle 916 ThomasE.Smith 22 MolecularCellBiology 919 22.1Overview 920 22.2NervousTissue:MetabolismandFunction 920 22.3TheEye:MetabolismandVision 932 22.4MuscleContraction 946 22.5MechanismofBloodCoagulation 960 ClinicalCorrelations 22.1LambertEatonMyasthenicSyndrome 927 22.2MyastheniaGravis:ANeuromuscularDisorder 929 22.3MaculaDegeneration:OtherCausesofVisionLoss 936 22.4NiemannPickDiseaseandRetinitisPigmentosa 938 22.5RetinitisPigmentosaResultingfromaDeNovoMutationinthe GeneCodingforPeripherin 940 22.6AbnormalitiesinColorPerception 946 22.7TroponinSubunitsAsMarkersforMyocardialInfarction 954 22.8VoltageGatedIonChannelopathies 956 22.9IntrinsicPathwayDefects:PrekallikreinDeficiency 963 22.10ClassicHemophilia 969 22.11ThrombosisandDefectsoftheProteinCPathway 971 RichardT.OkitaandBettieSueSilerMasters 23 Biotransformations:TheCytochromesP450 981 23.1Overview 982 23.2CytochromesP450:NomenclatureandOverallReaction 982 23.3CytochromesP450:MultipleForms 984 23.4InhibitorsofCytochromesP450 986 23.5CytochromeP450ElectronTransportSystems 987 23.6PhysiologicalFunctionsofCytochromesP450 989 23.7OtherHemoproteinandFlavoproteinMediatedOxygenations:The NitricOxideSynthases 995 ClinicalCorrelations 23.1ConsequencesofInductionofDrugMetabolizingEnzymes 986 23.2GeneticPolymorphismsofDrugMetabolizingEnzymes 987 23.3DeficiencyofCytochromeP450Steroid21Hydroxylase (CYP21A2) 992 23.4SteroidHormoneProductionduringPregnancy 993 23.5ClinicalAspectsofNitricOxideProduction 996 WilliamM.Awad,Jr. 24 IronandHemeMetabolism 1001 24.1IronMetabolism:Overview 1002 24.2IronContainingProteins 1003 24.3IntestinalAbsorptionofIron 1005 24.4MolecularRegulationofIronUtilization 1006 24.5IronDistributionandKinetics 1007 24.6HemeBiosynthesis 1009 24.7HemeCatabolism 1017 ClinicalCorrelations 24.1IronOverloadandInfection 1003 24.2DuodenalIronAbsorption 1005 24.3MutantIronResponsiveElement 1007 24.4CeruloplasminDeficiency 1008 24.5IronDeficiencyAnemia 1009 24.6Hemochromatosis:MolecularGeneticsandtheIssueofIron FortifiedDiets 1011 24.7AcuteIntermittentPorphyria 1013 24.8NeonatalIsoimmuneHemolysis 1020 24.9BilirubinUDPGlucuronosyltransferaseDeficiency 1020 24.10ElevationofSerumConjugatedBilirubin 1021 JamesBaggott 25 GasTransportandpHRegulation 1025 25.1IntroductiontoGasTransport 1026 25.2NeedforaCarrierofOxygeninBlood 1026 25.3HemoglobinandAllosterism:Effectof2,3Bisphosphoglycerate 1029 25.4OtherHemoglobins 1030 25.5PhysicalFactorsthatAffectOxygenBinding 1031 25.6CarbonDioxideTransport 1031 25.7InterrelationshipsamongHemoglobin,Oxygen,CarbonDioxide, HydrogenIon,and2,3Bisphosphoglycerate 1036 25.8IntroductiontopHRegulation 1036 25.9BufferSystemsofPlasma,InterstitialFluid,andCells 1036 25.10TheCarbonDioxideBicarbonateBufferSystem 1038 25.11AcidBaseBalanceanditsMaintenance 1041 25.12CompensatoryMechanisms 1046 25.13AlternativeMeasuresofAcidBaseImbalance 1049 25.14TheSignificanceofNa+ andCl inAcidBaseImbalance 1050 ClinicalCorrelations 25.1DiaspirinHemoglobin 1026 25.2Cyanosis 1028 20. Pagexxv 25.3ChemicallyModifiedHemoglobins:Methemoglobinand Sulfhemoglobin 1030 25.4HemoglobinswithAbnormalOxygenAffinity 1032 25.5TheCaseoftheVariableConstant 1039 25.6TheRoleofBoneinAcidBaseHomeostasis 1042 25.7AcuteRespiratoryAlkalosis 1047 25.8ChronicRespiratoryAcidosis 1048 25.9SalicylatePoisoning 1049 25.10EvaluationofClinicalAcidBaseData 1051 25.11MetabolicAlkalosis 1052 UlrichHopfer 26 DigestionandAbsorptionofBasicNutritionalConstituents 1055 26.1Overview 1056 26.2Digestion:GeneralConsiderations 1059 26.3EpithelialTransport 1063 26.4DigestionandAbsorptionofProteins 1070 26.5DigestionandAbsorptionofCarbohydrates 1073 26.6DigestionandAbsorptionofLipids 1077 26.7BileAcidMetabolism 1083 ClinicalCorrelations 26.1CysticFibrosis 1067 26.2BacterialToxigenicDiarrheasandElectrolyteReplacement Therapy 1068 26.3NeutralAminoAciduria(HartnupDisease) 1073 26.4DisaccharidaseDeficiency 1075 26.5CholesterolStones 1081 26.6AbLipoproteinemia 1082 StephenG.Chaney 27 PrinciplesofNutritionI:Macronutrients 1087 27.1Overview 1088 27.2EnergyMetabolism 1088 27.3ProteinMetabolism 1089 27.4ProteinEnergyMalnutrition 1093 27.5ExcessProteinEnergyIntake 1094 27.6Carbohydrates 1095 27.7Fats 1097 27.8Fiber 1097 27.9CompositionofMacronutrientsintheDiet 1098 ClinicalCorrelations 27.1VegetarianDietsandProteinEnergyRequirements 1091 27.2LowProteinDietsandRenalDisease 1092 27.3ProvidingAdequateProteinandCaloriesfortheHospitalized Patient 1093 27.4CarbohydrateLoadingandAthleticEndurance 1096 27.5HighCarbohydrateVersusHighFatDietsforDiabetics 1096 27.6PolyunsaturatedFattyAcidsandRiskFactorsforHeartDisease 1099 27.7MetabolicAdaptation:TheRelationshipbetweenCarbohydrate IntakeandSerumTriacylglycerols 1100 StephenG.Chaney 28 PrinciplesofNutritionII:Micronutrients 1107 28.1Overview 1108 28.2AssessmentofMalnutrition 1108 28.3RecommendedDietaryAllowances 1109 28.4FatSolubleVitamins 1109 28.5WaterSolubleVitamins 1118 28.6EnergyReleasingWaterSolubleVitamins 1119 28.7HematopoieticWaterSolubleVitamins 1123 28.8OtherWaterSolubleVitamins 1127 28.9Macrominerals 1128 28.10TraceMinerals 1130 28.11TheAmericanDiet:FactandFallacy 1132 28.12AssessmentofNutritionalStatusinClinicalPractice 1133 ClinicalCorrelations 28.1NutritionalConsiderationsforCysticFibrosis 1112 28.2RenalOsteodystrophy 1113 28.3NutritionalConsiderationsintheNewborn 1117 28.4AnticonvulsantDrugsandVitaminRequirements 1118 28.5NutritionalConsiderationsintheAlcoholic 1120 28.6VitaminB6 RequirementsforUsersofOralContraceptives 1124 28.7DietandOsteoporosis 1129 28.8NutritionalConsiderationsforVegetarians 1134 28.9NutritionalNeedsofElderlyPersons 1134 CarolN.Angstadt Appendix ReviewofOrganicChemistry 1137 Index 1149 21. Pagexxvii ChapterQuestionsandAnswers Thequestionsattheendofeachchapterareprovidedtohelpyoutestyourknowledgeandincreaseyourunderstandingofbiochemistry.Sincetheyareintendedto helpyoustrengthenyourknowledge,theirconstructiondoesnotalwaysconformtoprinciplesforassessingyourretentionofindividualfacts.Specifically,youwill sometimesbeexpectedtodrawonyourknowledgeofseveralareastoanswerasinglequestion,andsomequestionsmaytakelongertoanalyzethantheaveragetime allowedoncertainnationalexaminations.Occasionally,youmaydisagreewiththeanswer.Ifthisoccurs,wehopethatafteryoureadthecommentarythat accompaniestheanswertothequestion,youwillseethepointandyourinsightintothebiochemicalproblemwillbeincreased. Thequestiontypesconformtothosecurrentlyusedinobjectiveexaminations.Theyare: Type1:Choosetheonebestanswer Type2:Matchthenumberedstatementorphrasewithoneoftheletteredoptionsgivenabove. 22. Page1 Chapter1 EukaryoticCellStructure ThomasM.Devlin 1.1Overview:CellsandCellularCompartments 2 1.2CellularEnvironment:WaterandSolutes 4 HydrogenBondsFormbetweenWaterMolecules 4 WaterHasUniqueSolventProperties 5 SomeMoleculesDissociatewithFormationofCationsandAnions 5 WeakElectrolytesDissociatePartially 6 WaterIsaWeakElectrolyte 6 ManyBiologicallyImportantMoleculesAreAcidsorBases 7 TheHendersonHasselbalchEquationDefinestheRelationshipbetween pHandConcentrationsofConjugateAcidandBase 9 BufferingIsImportanttoControlpH 10 1.3OrganizationandCompositionofEukaryoticCells 12 ChemicalCompositionofCells 13 1.4FunctionalRoleofSubcellularOrganellesandMembraneSystems 15 PlasmaMembraneIstheLimitingBoundaryofaCell 16 NucleusIsSiteofDNAandRNASynthesis 16 EndoplasmicReticulumHasaRoleinManySyntheticPathways 16 TheGolgiApparatusIsInvolvedinSequesteringofProteins 17 MitochondriaSupplyMostCellNeedsforATP 17 LysosomesAreRequiredforIntracellularDigestion 17 PeroxisomesContainOxidativeEnzymesInvolvingHydrogenPeroxide 19 CytoskeletonOrganizestheIntracellularContents 19 CytosolContainsSolubleCellularComponents 20 Conclusion 20 Bibliography 20 QuestionsandAnswers 21 ClinicalCorrelations 1.1BloodBicarbonateConcentrationinMetabolicAcidosis 12 1.2MitochondrialDiseases:Luft'sDisease 16 1.3LysosomalEnzymesandGout 18 1.4LysosomalAcidLipaseDeficiency 19 1.5ZellwegerSyndromeandtheAbsenceofFunctionalPeroxisomes 20 23. Page2 1.1 Overview: CellsandCellularCompartments Overthreebillionyearsago,underconditionsnotentirelyclearandinatimespandifficulttocomprehend,elementssuchascarbon,hydrogen,oxygen,nitrogen,sulfur, andphosphorusformedsimplechemicalcompounds.Theycombined,dispersed,andrecombinedtoformavarietyoflargermoleculesuntilacombinationwas achievedthatwascapableofreplicatingitself.Thesemacromoleculesconsistedofsimplermoleculeslinkedtogetherbychemicalbonds.Withcontinuedevolutionand formationofevermorecomplexmolecules,thewaterenvironmentaroundsomeoftheseselfreplicatingmoleculesbecameenclosedbyamembrane.This developmentgavetheseprimordialstructurestheabilitytocontroltheirownenvironmenttosomeextent.Aformoflifehadevolvedandaunitofthreedimensional spaceacellhadbeenestablished.Withthepassingoftimeadiversityofcellsevolved,andtheirchemistryandstructurebecamemorecomplex.Theycould extractnutrientsfromtheenvironment,chemicallyconvertingthesenutrientstosourcesofenergyortocomplexmolecules,controlchemicalprocessesthatthey catalyzed,andcarryoutcellularreplication.Thusthevastdiversityoflifeobservedtodaybegan.Thecellisthebasicunitoflifeinallformsoflivingorganisms,fromthe smallestbacteriumtothemostcomplexanimal. Thelimitingoutermembraneofcells,theplasmamembrane,delineatesthespaceoccupiedbyacellandseparatesthevariableandpotentiallyhostileenvironment outsidefromtherelativelyconstantmilieuwithin.Itisthecommunicationlinkbetweenthecellanditssurroundings. Onthebasisofmicroscopicandbiochemicaldifferences,livingcellsaredividedintotwomajorclasses:prokaryotes,whichincludebacteria,bluegreenalgae,and rickettsiae,andeukaryotes,whichincludeyeasts,fungi,andplantandanimalcells.Prokaryoteshaveavarietyofshapesandsizes,inmostcasesbeing1/1000to 1/10,000thesizeofeukaryoticcells.Theylackintracellularmembraneboundstructuresthatcanbevisualizedbyamicroscope(Figure1.1).Thedeoxyribonucleic acid(DNA)ofprokaryotesisoftensegregatedintoadiscretemass,thenucleoidregion,thatisnotsurroundedbyamembraneorenvelope.Theplasmamembraneis ofteninvaginated.Incontrast,eukaryoticcellshaveawelldefinedmembranesurroundingacentralnucleusandavarietyofintracellularstructuresandorganelles (Figure1.1b).Intracellularmembranesystemsestablishdistinctsubcellularcompartments,asdescribedinSection1.4,thatpermitauniquedegreeofsubcellular specialization.Bycompartmentalizationdifferentchemicalreactionsthatrequiredifferentenvironmentscanoccursimultaneously.Manyreactionsoccurinoron specificmembranes,thuscreatinganadditionalenvironmentforthediversefunctionsofcells. Besidesthesestructuralvariationsbetweenprokaryoticandeukaryoticcells(Figures1aand1b),therearedifferencesinchemicalcompositionandbiochemical activities.Prokaryoteslackhistones,aclassofproteinsthatcomplexwithDNAineukaryotes.Therearemajorstructuraldifferencesintheribonucleicacidprotein complexesinvolvedinbiosynthesisofproteinsbetweenthecelltypes,aswellasdifferencesintransportmechanismsacrosstheplasmamembraneandinenzyme content.Themanysimilarities,however,areequallystriking.Theemphasisthroughoutthisbookisonthechemistryofeukaryotes,particularlymammaliancells,but muchofourknowledgeofthebiochemistryoflivingcellshascomefromstudiesofprokaryoticandnonmammalianeukaryoticcells.Thebasicchemicalcomponents andfundamentalchemicalreactionsofalllivingcellsareverysimilar.Availabilityofcertaincellpopulations,forexample,bacteriaincontrasttohumanliver,hasledto muchofourknowledgeaboutsomecellsinsomeareasourknowledgeisderivednearlyexclusivelyfromstudiesofprokaryotes.Theuniversalityofmanybiochemical phenomena,however,permitsmanyextrapolationsfrombacteriatohumans. 24. Page3 Figure1.1 Cellularorganizationofprokaryoticandeukaryoticcells. (a)ElectronmicrographofEscherichiacoli,arepresentative prokaryoteapproximatemagnification30,000.Thereislittle apparentintracellularorganizationandnocytoplasmicorganelles. Chromatiniscondensedinanuclearzonebutnotsurroundedbya membrane.Prokaryoticcellsaremuchsmallerthaneukaryoticcells. (b)Electronmicrographofathinsectionofalivercell(rathepatocyte), arepresentativeeukaryoticcellapproximatemagnification 7500.Notethedistinctnuclearmembrane,different membraneboundorganellesorvesicles,andextensivemembranesystems. Variousmembranescreateavarietyofintracellularcompartments. Photograph(a)generouslysuppliedbyDr.M.E.Bayer,FoxChaseCancer Institute,Philadelphia,PAphotograph (b)reprintedwithpermissionof Dr.K.R.Porter,fromPorter,K.R.,andBonneville,M.A.In: FineStructureofCellsandTissues.Philadelphia:Lea&Febiger,1972. 25. Page4 Beforewedissectthecomplexitiesofmammaliancellsandtissuesinthefollowingchapters,itisappropriatetoreviewsomeofthechemicalandphysical characteristicsoftheenvironmentinwhichthevariousbiochemicalphenomenaoccur.Thisenvironmentplacesmanyconstraintsonthecell'sactivities.Theconcluding sectionoutlinestheactivitiesandrolesofsubcellularcompartments. Figure1.2 Structureofawatermolecule. TheHOHbondangleis104.5.Bothhydrogen atomscarryapartialpositivecharge andtheoxygenapartialnegative charge,creatingadipole. 1.2 CellularEnvironment: WaterandSolutes Allbiologicalcellscontainessentiallythesamebuildingblocksandtypesofmacromolecules.ThegeneralclassesofsubstancesincellsarepresentedinTable1.1. Therearesignificantvariationsinconcentrationofspecificcomponentsindifferentcelltypesandinorganellesofeukaryoticcells.Microenvironmentsarealso createdbymacromoleculesandmembranesinwhichthecompositiondiffersfromthatofthesurroundingmilieu.Cellsdependontheexternalenvironmentfornutrients requiredforreplacementofcomponents,growth,andenergyneeds.Theyhaveavarietyofmechanismstocopewithvariationsincompositionoftheexternal environment.Wateristheonecommoncomponentofallenvironments.Itisthesolventinwhichthesubstancesrequiredforthecell'sexistencearedissolvedor suspended.Theuniquephysicochemicalpropertiesofwatermakelifeonearthpossible. HydrogenBondsFormbetweenWaterMolecules Twohydrogenatomssharetheirelectronswithanunsharedpairofelectronsofanoxygenatomtoformawatermolecule.Theoxygennucleushasastronger attractionforsharedelectronsthanhydrogen,andpositivelychargedhydrogennucleiareleftwithanunequalshareofelectrons,creatingapartialpositivechargeon eachhydrogenandapartialnegativechargeonoxygen.Thebondanglebetweenhydrogensandoxygenis104.5,makingthemoleculeelectricallyasymmetricand producinganelectricdipole(Figure1.2).Watermoleculesinteractbecausepositivelychargedhydrogenatomsononemoleculeareattractedtothenegativelycharged oxygenatomonanother,withformationofaweakbondbetweentwowatermolecules(Figure1.3a).Thisbond,indicatedbyadashedline,isahydrogenbond.A detaileddiscussionofnoncovalentinteractionsbetweenmolecules,includingelectrostatic,vanderWaals,andhydrophobic,ispresentedonpage64.Fivemoleculesof waterformatetrahedralstructure(Figure1.3b),becauseeachoxygensharesitselectronswithfourhydrogenatomsandeachhydrogenwithanotheroxygen.A tetrahedrallatticestructureisformediniceandgivesiceitscrystallinestructure.Somehydrogenbondsarebrokenasiceistransformedtoliquidwater.Eachbondis relatively Figure1.3 Hydrogenbonding. (a)Hydrogenbonding, indicatedbydashed lines,betweentwowater molecules. (b)Tetrahedral hydrogenbondingoffive watermolecules.Water molecules1,2,and3 areintheplaneofthe page,4isbelow,and 5isabove. TABLE1.1ChemicalComponentsofBiologicalCells Component RangeofMolecular Weights H2 O 18 Inorganicions 23100 Na+ ,K+ ,Cl ,SO4 2 ,HCO3 Ca2+ , Mg2+ ,etc. Smallorganicmolecules 1001200 Carbohydrates,aminoacids,lipids, nucleotides,peptides Macromolecules 50,0001,000,000,000 Proteins,polysaccharides,nucleic acids 26. Page5 weakcomparedtoacovalentbondbutthelargenumberofhydrogenbondsbetweenmoleculesinliquidwateristhereasonforthestabilityofwater.Liquidwater actuallyhasadefinitestructureduetohydrogenbondingthatisinadynamicstateasthesebondsbreakandreform.Hydrogenbondsinwaterhaveahalflifeofless than11010 s.Liquidwatercontainsasignificantnumberofhydrogenbondsevenat100C,whichaccountsforitshighheatofvaporizationinthetransformation fromliquidtovaporstate,hydrogenbondsaredisrupted. Watermoleculeshydrogenbondtodifferentchemicalstructures.Hydrogenbondingalsooccursbetweenothermoleculesandwithinamoleculewherever electronegativeoxygenornitrogencomesincloseproximitytohydrogencovalentlybondedtoanotherelectronegativeatom.Representativehydrogenbondsare presentedinFigure1.4.Intramolecularhydrogenbondingoccursextensivelyinlargemacromoleculessuchasproteinsandnucleicacidsandispartiallyresponsiblefor theirstructuralstability. Manymodelsforthestructureofliquidwaterhavebeenproposed,butnoneadequatelyexplainsallitsproperties. WaterHasUniqueSolventProperties Thepolarnatureandabilitytoformhydrogenbondsarethebasisfortheuniquesolventpropertiesofwater.Polarmoleculesarereadilydispersedinwater.Saltsin whichacrystallatticeisheldtogetherbyattractionofpositiveandnegativegroupsdissolveinwaterbecauseelectrostaticforcesinthecrystalcanbeovercomeby attractionofchargestothedipoleofwater.NaClisanexamplewhereelectrostaticattractionofindividualNa+andClatomsisovercomebyinteractionofNa+with thenegativechargeonoxygenatoms,andClwithpositivechargesonthehydrogenatoms.Thusashellofwatersurroundstheindividualions.Thenumberofweak chargechargeinteractionsbetweenwaterandNa+andClionsissufficienttoseparatethetwochargedions. Manyorganicmoleculesthatcontainnonionicbutweaklypolargroupsaresolubleinwaterbecauseofattractionofthesegroupstomoleculesofwater.Sugarsand alcoholsarereadilysolubleinwaterforthisreason.Amphipathicmolecules,compoundsthatcontainbothpolarandnonpolargroups,disperseinwaterifattractionof thepolargroupforwatercanovercomehydrophobicinteractionsofnonpolarportionsofthemolecules.Veryhydrophobicmolecules,suchascompoundsthatcontain longhydrocarbonchains,however,donotreadilydisperseassinglemoleculesinwaterbutinteractwithoneanothertoexcludethepolarwatermolecules. Figure1.4 Representativehydrogen bondsof importanceinbiologicalsystems. SomeMoleculesDissociatewithFormationofCationsandAnions Substancesthatdissociateinwaterintoacation(positivelychargedion)andananion(negativelychargedion)areclassifiedaselectrolytes.Thepresenceof chargedionsfacilitatesconductanceofanelectricalcurrentthroughanaqueoussolution.Sugarsoralcohols,whichreadilydissolveinwaterbutdonotcarryacharge ordissociateintochargedspecies,areclassifiedasnonelectrolytes. Figure1.5 Reactionsthatoccurwhensodium lactateisdissolvedinwater. Saltsofalkalimetals(e.g.,Li,Na,andK),dissolvedinwateratlowconcentrations,dissociatecompletelyathighconcentrations,however,thereisincreasedpotential forinteractionofanionsandcations.Withbiologicalsystemsitiscustomarytoconsidersuchcompoundsastotallydissociatedbecausetheirconcentrationsarelow. Saltsoforganicacids,forexample,sodiumlactate,alsodissociatetotallyandareclassifiedaselectrolytesthedissociatedanion,lactateion,reactstoalimitedextent withaprotontoformundissociatedacid(Figure1.5).Whensuchsaltsaredissolvedinwater,individualionsarepresentinsolutionratherthantheundissociatedsalt. Ifasolutionhasbeenpreparedwith 27. Page6 severaldifferentsalts(e.g.,NaCl,K2SO4,andNalactate),theoriginalmoleculesdonotexistassuchinsolution,onlytheions(e.g.,Na+ ,K+ ,SO42andlactate). Manyacids,however,whendissolvedinwaterdonottotallydissociatebutratherestablishanequilibriumbetweenundissociatedanddissociatedcomponents.Thus lacticacid,animportantmetabolicintermediate,partiallydissociatesintolactateanionsandH+ asfollows: Becauseoftheirpartialdissociation,however,suchcompoundshavealowercapacitytocarryanelectricalchargeonamolarbasiswhencomparedtothosethat dissociatetotallytheyaretermedweakelectrolytes. WeakElectrolytesDissociatePartially Inpartialdissociationofaweakelectrolyte,representedbyHA,theconcentrationofthevariousspeciescanbedeterminedfromtheequilibriumequation: A representsthedissociatedanionandsquarebracketsindicateconcentrationofeachcomponentinconcentrationunitssuchasmolesperliter(molL1 )ormillimol L1 .Theactivityofeachspeciesratherthanconcentrationshouldbeemployedintheequilibriumequationbutsincemostcompoundsofinterestinbiologicalsystems arepresentinlowconcentration,thevalueforactivityapproachesthatofconcentration.Thustheequilibriumconstantisindicatedas cannotbedetermined becauseatequilibriumthereisnoremainingundissociatedsolute. WaterIsaWeakElectrolyte Waterdissociatesasfollows: Aprotonthatdissociatesinteractswithoxygenofanotherwatermoleculetoformthehydroniumion,H3O+ .Forconvenience,inthisbooktheprotonwillbepresented asH+ ratherthanH3 O+ ,eventhoughthelatteristheactualchemicalspecies.At25Cthevalueof fordissociationofwaterisverysmallandisabout1.81016 : Withsuchasmall aninsignificantnumberofwatermoleculesactuallydissociaterelativetothenumberofundissociatedmolecules.Thustheconcentrationofwater, whichis55.5M,isessentiallyunchanged.Equation1.1canberewrittenasfollows: isaconstantandistermedtheionproductofwater.Itsvalueat25Cis11014 .InpurewatertheconcentrationofH+ equalsOH ,andby substituting[H+]for[OH]intheequationabove,[H+]is1107M.Similarly, 28. Page7 [OH]isalso1107M.TheequilibriumofH2 O,H+,andOHalwaysexistsindilutesolutionsregardlessofthepresenceofdissolvedsubstances.Ifdissolved materialalterseithertheH+orOHconcentration,asoccursonadditionofanacidorbase,aconcomitantchangeintheotherionmustoccurinordertosatisfythe equilibriumrelationship.Byusingtheequationfortheionproduct,[H+]or[OH]canbecalculatedifconcentrationofoneoftheionsisknown. TABLE1.2RelationshipsBetween[H+]andpHand [OH ]andpOH [H+ ](M) pH [OH ](M) pOH 1.0 0 11014 14 0.1(1101) 1 11013 13 1102 2 11012 12 1103 3 11011 11 1104 4 11010 10 1105 5 1109 9 1106 6 1108 8 1107 7 1107 7 1108 8 1106 6 1109 9 1105 5 11010 10 1104 4 11011 11 1103 3 11012 12 1102 2 11013 13 0.1(1101 ) 1 11014 14 1.0 0 Theimportanceofhydrogenionsinbiologicalsystemswillbecomeapparentinsubsequentchapters.Forconvenience[H+ ]isusuallyexpressedintermsofpH, calculatedasfollows: Inpurewater[H+]and[OH]areboth1107M,andpH=7.0.[OH]isexpressedasthepOH.Fortheequationdescribingdissociationofwater,11014= [H+][OH]takingnegativelogarithmsofbothsides,theequationbecomes14=pH+pOH.Table1.2presentstherelationshipbetweenpHand[H+]. ThepHvaluesofdifferentbiologicalfluidsarepresentedinTable1.3.Inbloodplasma,[H+]is0.00000004MorapHof7.4.Othercationsarebetween0.001and 0.10M,wellover10,000timeshigherthan[H+ ].Anincreaseinhydrogenionto0.0000001M(pH7.0)leadstoseriousmedicalconsequencesandislifethreatening adetaileddiscussionofmechanismsbywhichthebodymaintainsintraandextracellularpHispresentedinChapter25. ManyBiologicallyImportantMoleculesAreAcidsorBases ThedefinitionsofanacidandabaseproposedbyLowryandBrnstedaremostconvenientinconsideringbiologicalsystems.Anacidisaprotondonorandabase isaprotonacceptor.Hydrochloricacid(HCl)andsulfuricacid(H2 SO4 )arestrongacidsbecausetheydissociatetotally,andOHionisabasebecauseitacceptsa proton,shiftingtheequilibrium WhenastrongacidandOH arecombined,H+ fromtheacidandOH interactandareinequilibriumwithH2O.NeutralizationofH+ andOH occursbecausetheion productforwaterissosmall. Anionsproducedwhenstrongacidsdissociatetotally,suchasCl fromHCl,arenotbasesbecausetheydonotassociatewithprotonsinsolution.Whenanorganic acid,suchaslacticacid,isdissolvedinwateritdissociatesonlypartially,establishinganequilibriumbetweenanacid(protondonor),ananionoftheacid,andaproton asfollows: Lacticacidisaweakacid.Theanionisabasebecauseitacceptsaprotonandreformstheacid.Theweakacidandthebaseformedondissociationarereferredto asaconjugatepairotherexamplesarepresentedinTable1.4.Ammoniumion(NH4 + )isanacidbecauseitdissociatestoyieldH+ andammonia(NH3),an unchargedspecies,whichisaconjugatebase.Phosphoricacid(H3 PO4 )isanacidandPO4 3isabase,butH2 PO4 andHPO4 2areeitherabaseoraciddepending onwhetherthephosphategroupisacceptingordonatingaproton. TABLE1.3pHofSomeBiologicalFluids Fluid pH Bloodplasma 7.4 Interstitialfluid 7.4 Intracellularfluid Cytosol(liver) 6.9 Lysosomalmatrix Below5.0 Gastricjuice 1.53.0 Pancreaticjuice 7.88.0 Humanmilk 7.4 Saliva 6.47.0 Urine 5.08.0 ThetendencyofaconjugateacidtodissociateH+canbeevaluatedfromthe of11014at25C. Aconvenientmethodofstatingthe isintheformofpK,as 29. Page8 TABLE1.4SomeConjugateAcidBasePairsofImportanceinBiological Systems ProtonDonor(Acid) ProtonAcceptor(Base) CH3 CHOHCOOH H++CH3 CHOHCOO (lacticacid) (lactate) CH3COCOOH H+ +CH3COCOO (pyruvicacid) (pyruvate) HOOCCH2 CH2 COOH 2H++OOCCH2 CH2 COO (succinicacid) (succinate) + H3NCH2COOH H+ ++ H3NCH2COO (glycine) (glycinate) H3 PO4 H++H2 PO4 H2 PO4 H++HPO42 HPO4 2 H++PO4 3 Glucose6PO3 H H++glucose6PO32 H2 CO3 H++HCO3 NH4 + H+ +NH3 H2 O H++OH NotethesimilarityofthisdefinitionwiththatofpHaswithpHand[H+],therelationshipbetweenpK and andpK forconjugateacidsofimportanceinbiological systemsarepresentedinTable1.5. Aspecialcaseofaweakacidimportantinmedicineiscarbonicacid(H2 CO3 ).Carbondioxidewhendissolvedinwaterisinvolvedinthefollowingequilibrium reactions: TABLE1.5ApparentDissociationConstantandpKofSomeCompoundsofImportanceinBiochemistry Compound (M) pK Aceticacid (CH3 COOH) 1.74105 4.76 Alanine 4.57103 2.041010 2.34(COOH) 9.69(NH3+) Citricacid 8.12104 1.77105 3.89106 3.09 3.74 5.41 Glutamicacid 6.45103 5.62105 2.141010 2.19(COOH) 4.25(COOH) 9.67(NH3+) Glycine 4.57103 2.511010 2.34(COOH) 9.60(NH3+) Lacticacid (CH3CHOHCOOH) 1.38104 3.86 Pyruvicacid (CH3COCOOH) 3.16103 2.50 Succinicacid (HOOCCH2CH2COOH) 6.46105 4.19 3.31106 5.48 Glucose6PO3H 7.76107 6.11 H3PO4 1102 2.0 H2PO4 2.0107 6.7 HPO4 2 3.41013 12.5 H2 CO3 1.70104 3.77 NH4 + 5.621010 9.25 H2 O 11014 14.0 30. Page9 Carbonicacidisarelativelystrongacidwitha of3.77.Theequilibriumequationforthisreactionis Carbonicacidis,however,inequilibriumwithdissolvedCO2 andtheequilibriumequationforthisreactionis SolvingEq.1.6forH2CO3andsubstitutingfortheH2CO3inEq.1.5,thetwoequilibriumreactionsarecombinedintooneequation: Rearrangingtocombineconstants,includingtheconcentrationofH2 O,simplifiestheequationandyieldsanewcombinedconstant, ,asfollows: ItiscommonpracticetorefertodissolvedCO2 asaconjugateaciditistheacidanhydrideofH2 CO3 .Theterm hasavalueof7.95107 and .Ifthe aqueoussystemisincontactwithanairphase,dissolvedCO2 willalsobeinequilibriumwithCO2 intheairphase.Adecreaseorincreaseofonecomponentthatis, CO2 (air),CO2 (dissolved),H2 CO3 ,H+ or willcauseachangeinalltheothercomponents. 000906.gif 000907.gif TheHendersonHasselbalchEquationDefinestheRelationshipbetweenpHandConcentrationsofConjugateAcidandBase Achangeinconcentrationofanycomponentinanequilibriumreactionnecessitatesaconcomitantchangeineverycomponent.Forexample,anincreasein[H+ ]will decreasetheconcentrationofconjugatebase(e.g.,lactateion)withanequivalentincreaseintheconjugateacid(e.g.,lacticacid).Thisrelationshipisconveniently expressedbyrearrangingtheequilibriumequationandsolvingforH+ ,asshownforthefollowingdissociation: RearrangingEq.1.9bydividingthroughbyboth[H+ ]and leadsto Takingthelogarithmofbothsidesgives SincepH=log1/[H+ ]and Eq.1.11becomes Equation1.12,developedbyHendersonandHasselbalch,isaconvenientwayofviewingtherelationshipbetweenpHofasolutionandrelativeamountsofconjugate baseandacidpresent.AnalysisofEq.1.12demonstratesthatwhentheratioof[base]/[acid]is1:1,pHequalsthepK oftheacidbecauselog1=0, 31. Page10 Figure1.6 Ratioofconjugate[base]/[acid]asa functionofthepH. Whentheratioof[base]/[acid]is1,pH equalspK ofweakacid. andthuspH=pK .IfpHisoneunitlessthanpK ,the[base]/[acid]ratiois1:10,andifpHisoneunitabovepK ,the[base]/[acid]ratiois10:1.Figure1.6isaplot ofratiosofconjugatebasetoconjugateacidversuspHofseveralweakacidsnotethatratiosarepresentedonalogarithmicscale. BufferingIsImportanttoControlpH WhenNaOHisaddedtoasolutionofaweakacidsuchaslacticacid,theratioof[conjugatebase]/[conjugateacid]changes.NaOHdissociatestotallyandtheOH formedisneutralizedbyexistingH+ toformH2 O.Thedecreasein[H+ ]willcausefurtherdissociationofweakacidtocomplywithrequirementsofitsequilibrium reaction.TheamountofweakaciddissociatedwillbesonearlyequaltotheamountofOH addedthatitisconsideredtobeequal.Thusthedecreaseinamountof conjugateacidisequaltotheamountofconjugatebasethatisformed.TheseseriesofeventsarerepresentedintitrationcurvesoftwoweakacidspresentedinFigure 1.7.When0.5equivofOH isadded,50%oftheweakacidisdissociatedandthe[acid]/[base]ratiois1.0pHatthispointisequaltopK oftheacid.Shapesof individualtitrationcurvesaresimilarbutdisplacedduetodifferencesinpK values.ThereisarathersteepriseinpHwhenonly0.1equivofOH areadded,but between0.1and0.9equivofaddedOH ,thepHchangeisonly~2.ThusalargeamountofOH isaddedwitharelativelysmallchangeinpH.Thisiscalled bufferingandisdefinedastheabilityofasolutiontoresistachangeinpHwhenanacidorbaseisadded.Ifweakacidwerenotpresent,thepHwouldbeveryhigh withonlyasmallamountofOH becausetherewouldbenosourceofH+ toneutralizetheOH . ThebestbufferingrangeforaconjugatepairisinthepHrangenearthepK oftheweakacid.StartingfromapHoneunitbelowtoapHoneunitabovepK ,~82% ofaweakacidinsolutionwilldissociate,andthereforeanamountofbaseequivalenttoabout82%oforiginalacidcanbeneutralizedwithachangeinpHof2.The maximumbufferingrangeforaconjugatepairisconsideredtobebetween1pHunitaboveandbelowthepK .LacticacidwithpK =3.86isaneffectivebufferinthe rangeofpH3to5buthasnobufferingcapacityatpH=7.0.TheHPO4 2 /H2 PO4 pairwithpK =6.7,however,isaneffectivebufferatpH=7.0.ThusatthepHof thecell'scytosol(~7.0),thelactatelacticacidpairisnotaneffectivebufferbutthephosphatesystemis. Figure1.7 Acidbasetitrationcurvesforlacticacid (pK3.86)andNH4 +(pK9.25). AtpHequaltorespective pK values,therewill beanequalamountofacidandbasefor eachconjugatepair. Bufferingcapacityalsodependsontheconcentrationsofconjugateacidandbase.Thehighertheconcentrationofconjugatebase,themoreaddedH+ withwhichit canreact.ThemoreconjugateacidthemoreaddedOH canbe 32. Page11 neutralizedbythedissociationoftheacid.AcaseinpointisbloodplasmaatpH7.4.ForHPO4 2 /H2PO4 thepK of6.7wouldsuggestthatthisconjugatepairwould beaneffectivebuffertheconcentrationofthephosphatepair,however,islowcomparedtothatoftheHCO3 /CO2 systemwithapK of6.1,whichispresentata 20foldhigherconcentrationandaccountsformostofthebufferingcapacity.InconsideringthebufferingcapacityboththepK andtheconcentrationoftheconjugate pairmustbetakenintoaccount.MostorganicacidsarerelativelyunimportantasbuffersincellularfluidsbecausetheirpK valuesaremorethanseveralpHunitslower thanthepHofthecell,andtheirconcentrationsaretoolowincomparisontosuchbuffersasHPO4 2 /H2 PO4 andtheHCO3 /CO2 system. TheimportanceofpHandbuffersinbiochemistryandclinicalmedicinewillbecomeapparent,particularlyinChapters2,4,and25.Figure1.8presents Figure1.8 TypicalproblemsofpHandbuffering. 33. Page12 sometypicalproblemsusingtheHendersonHasselbalchequationandClin.Corr.1.1isarepresentativeproblemencounteredinclinicalpractice. CLINICALCORRELATION1.1 BloodBicarbonateConcentrationinMetabolicAcidosis BloodbuffersinanormaladultcontrolbloodpHatabout7.40ifthepHshoulddrop below7.35,theconditionisreferredtoasanacidosis.AbloodpHofnear7.0could leadtoseriousconsequencesandpossiblydeath.Thusinacidosis,particularlythat causedbyametabolicchange,itisimportanttomonitortheacidbaseparametersofa patient'sblood.ValuesofinteresttoaclinicianincludethepHandHCO3 andCO2 concentrations.NormalvaluesforthesearepH=7.40,[HCO3 ]=24.0mM,and[CO2] =1.20mM. BloodvaluesofapatientwithametabolicacidosiswerepH=7.03and[CO2]=1.10 mM.Whatisthepatient'sblood[HCO3 ]andhowmuchofthenormal[HCO3 ]has beenusedinbufferingtheacidcausingthecondition? 1.TheHendersonHasselbalchequationis ThepK valuefor[HCO3 ]/[CO2]is6.10. 2.Substitutethegivenvaluesintheequation. or Theantilogof0.93is8.5thus or 3.Sincethenormalvalueof[HCO3 ]is24mM,therehasbeenadecreaseof14.6mmol ofHCO3 perliterofbloodinthispatient.IfmuchmoreHCO3 islost,apointwouldbe reachedwhenthisimportantbufferwouldbeunavailabletobufferanymoreacidinthe bloodandthepHwoulddroprapidly.InChapter25thereisadetaileddiscussionofthe causesandcompensationsthatoccurinsuchconditions. 1.3 OrganizationandCompositionofEukaryoticCells Asdescribedabove,eukaryoticcellsareorganizedintocompartments,eachdelineatedbyamembrane(Figure1.9).Thesearewelldefinedcellularorganellessuchas nucleus,mitochondria,lysosomes,andperoxisomes.Membranesalsoformatubulelikenetworkthroughoutthecellenclosinganinterconnectingspaceorcisternae, asisthecaseoftheendoplasmicreticulumorGolgicomplex.AsdescribedinSection1.4,thesecompartmentshavespecificfunctionsandactivities. Thesemipermeablenatureofcellularmembranespreventsthereadydiffusionofmanymoleculesfromonesidetotheother.Specificmechanismsinmembranesfor translocationoflargeandsmall,chargedandunchargedmoleculesallowmembranestomodulateconcentrationsofsubstancesinvariouscompartments. Macromolecules,suchasproteinsandnucleicacids,donotcrossbiologicalmembranesunlessthereisaspecificmechanismfortheirtranslocationorthemembraneis damaged.Thusthefluidmatrixofvariouscellularcompartmentshasadistinctivecompositionofinorganicions,organicmolecules,andmacromolecules.Partitioningof activitiesandcomponentsinmembraneenclosedcompartmentsandorganelleshasanumberofadvantagesfortheeconomyofthecell.Theseincludethesequestering ofsubstratesandcofactorswheretheyarerequired,andadjustmentsofpHandioniccompositionformaximumactivityofbiologicalprocesses. Theactivitiesandcompositionofcellularstructuresandorganelleshavebeendeterminedwithintactcellsbyavarietyofhistochemical,immunological,andfluorescent stainingmethods.Continuousobservationinrealtimeofcellulareventsinintactviablecellsispossible.Examplesarestudiesthatinvolvechangesofioniccalcium concentrationinthecytosolbytheuseoffluorescentcalciumindicators.Individualorganelles,membranes,andcomponentsofthecytosolcanbeisolatedandanalyzed followingdisruptionoftheplasmamembrane.Permeabilityoftheplasmamembranecanbealteredtopermitthereleaseofsubcellularcomponents.Techniquesfor disruptingmembranesincludeuseofdetergents,osmoticshock,andhomogenizationoftissues,whereshearingforcesbreakdowntheplasmamembrane.Inan appropriateisolationmedium,cellorganellesandmembranesystemscanbeseparatedbycentrifugationbecauseofdifferencesinsizeanddensity.Chromatographic procedureshavebeenemployedforisolationofindividualcellularfractionsandcomponents.Thesetechniqueshavepermittedisolationofcellularfractionsfrommost mammaliantissues.Inaddition,componentsoforganellessuchasnucleiandmitochondriacanbeisolatedfollowingdisruptionoftheorganellemembrane. Inmanyinstancestheisolatedstructuresandcellularfractionsappeartoretainthechemicalandbiochemicalcharacteristicsofthestructureinsitu.Butbiological membranesystemsareverysensitivestructures,subjecttodamageevenunderverymildconditions,andalterationscanoccurduringisolation,whichcanleadto changeincompositionofthestructure.Theslightestdamagetoamembranealtersitspermeabilityproperties,allowingsubstancesthatwouldnormallybeexcludedto traversethemembranebarrier.Inaddition,manyproteinsareonlylooselyassociatedwithmembranesandeasilydissociatewhendamageoccurs(seep.186). Notunexpectedly,therearedifferencesinstructure,composition,andactivitiesofcellsfromdifferenttissuesduetothediversefunctionsoftissues.Majorbiochemical activitiesofthecellularorganellesandmembranesystems,however,arefairlyconstantfromtissuetotissue.Thusbiochemicalpathwaysinliverareoftenpresentin othertissues.Thedifferencesbetweencelltypesare 34. Page13 Figure1.9 (a)Electronmicrographofaratlivercelllabeledtoindicatethemajor structuralcomponentsofeukaryoticcellsand (b)aschematicdrawingofananimalcell. Notethenumberandvarietyofsubcellularorganelles andthenetworkofinterconnectingmembranesenclosingchannels,thatis, cisternae.Alleukaryoticcellsarenotascomplexintheirappearance,but mostcontainthemajorstructuresshowninthefigure.ER,endoplasmic reticulumG,Golgizone,Ly,lysosomes,P,peroxisomesM,mitochondria. Photograph(a)reprintedwithpermissionofDr.K.R.PorterfromPorter, K.R.,andBonneville,M.A.In:FineStructureofCellsandTissues. Philadelphia:Lea&Febiger,1972schematic (b)reprintedwithpermissionfromVoet,D.,andVoet, J.G.Biochemistry,2nded.NewYork:Wiley,1995. usuallyindistinctivespecializedactivities.Evenwithinonetissue,cellsofdifferentoriginhavequalitativeandquantitativedifferencesincellorganellecomposition. ChemicalCompositionofCells Eachcellularcompartmenthasanaqueousfluidormatrixthatcontainsvariousions,smallmolecularweightorganicmolecules,differentproteins,andnucleicacids. Localizationofspecificmacromolecules,suchasenzymes,hasbeen 35. Page14 Figure1.10 Majorchemicalconstituentsofbloodplasma andcellfluid. Heightoflefthalfofeachcolumnindicates totalconcentrationofcationsthatofrighthalf, concentrationsofanions.Bothareexpressedin milliequivalentsperliter(meqL1 )offluid.Notethat chlorideandsodiumvaluesincellfluidarequestioned. Itisprobablethat,atleastinmuscle,thecytosol containssomesodiumbutnochloride. AdaptedfromGregersen,M.I.In:P.Bard(Ed.), MedicalPhysiology,11thed.StLouis,MO: Mosby,1961,p.307. determinedbuttheexactioniccompositionofthematrixoforganellesisstilluncertain.EachhasadistinctlydifferentioniccompositionandpH.Theoverallionic compositionofintracellularfluid,consideredtorepresentthecytosolprimarily,comparedtobloodplasmaispresentedinFigure1.10.Na+ isthemajorextracellular cation,withaconcentrationof~140meqL1(mM)verylittleNa+ispresentinintracellularfluid.K+isthemajorintracellularcation.Mg2+ispresentinbothextra andintracellularcompartmentsatconcentrationsmuchlowerthanNa+ andK+ .ThemajorextracellularanionsareCl andHCO3withloweramountsofphosphateand sulfate.MostproteinshaveanegativechargeatpH7.4(Chapter2),beinganionsatthepHoftissuefluids.Majorintracellularanionsareinorganicphosphate,organicphosphates,and proteins.Otherinorganicandorganicanionsandcationsarepresentinconcentrationswellbelowthemilliequivalentperliter(millimolar)level.Exceptforverysmalldifferencescreatedby membranesandleadingtodevelopmentofmembranepotentials,thetotalanionconcentrationequalsthetotalcationconcentrationinthedifferentfluids. Intracellularconcentrationsofmostsmallmolecularweightorganicmolecules,suchassugars,organicacids,aminoacids,andphosphorylatedintermediates,areinthe rangeof0.011.0mMbutcanhavesignificantlylowerconcentrations.Coenzymes,organicmoleculesrequiredforactivityofsomeenzymes,areinthesamerangeof concentration.Substratesforenzymesarepresentinrelativelylowconcentrationincontrasttoinorganicions,butlocalizationina 36. Page15 specificorganelleorcellularmicroenvironmentcanincreasetheirconcentrationssignificantly. Itisnotverymeaningfultodeterminethemolarconcentrationofindividualproteinsincells.Inmanycasestheyarelocalizedwithspecificstructuresorincombination withotherproteinstocreateafunctionalunit.Itisinarestrictedcompartmentthatindividualproteinscarryouttheirrole,whetherstructural,catalytic,orregulatory. 1.4 FunctionalRoleofSubcellularOrganellesandMembraneSystems Thesubcellularlocalizationofvariousmetabolicpathwayswillbedescribedthroughoutthisbook.Insomecasesanentirepathwayislocatedinasinglecompartment butmanyaredividedbetweentwolocations,withtheintermediatesinthepathwaymovingorbeingtranslocatedfromonecompartmenttoanother.Ingeneral, organelleshaveveryspecificfunctionsandtheenzymaticactivitiesinvolvedareusedtoidentifythemduringisolation. Thefollowingdescribesbrieflysomemajorrolesofeukaryoticcellstructurestoindicatethecomplexityandorganizationofcells.Asummaryoffunctionsanddivision oflaborwithineukaryoticcellsispresentedinTable1.6andthestructuresarepresentedinFigure1.9. TABLE1.6SummaryofEukaryoticCellCompartmentsandTheirMajorFunctions Compartment MajorFunctions Plasmamembrane Transportofionsandmolecules Recognition Receptorsforsmallandlargemolecules Cellmorphologyandmovement Nucleus DNAsynthesisandrepair RNAsynthesis Nucleolus RNAprocessingandribosomesynthesis Endoplasmicreticulum Membranesynthesis Synthesisofproteinsandlipidsforsomeorganelles andforexport Lipidsynthesis Detoxicationreactions Golgiapparatus Modificationandsortingofproteinsfor incorporationintoorganellesandforexport Exportofproteins Mitochondria Energyconservation Cellularrespiration Oxidationofcarbohydratesandlipids Ureaandhemesynthesis Lysosomes Cellulardigestion:hydrolysisofproteins, carbohydrates,lipids,andnucleicacids Peroxisomes OxidativereactionsinvolvingO2 UtilizationofH2 O2 Microtubulesandmicrofilaments Cellcytoskeleton Cellmorphology Cellmotility Intracellularmovements Cytosol Metabolismofcarbohydrates,lipids,aminoacids, andnucleotides Proteinsynthesis 37. Page16 CLINICALCORRELATION1.2 MitochondrialDiseases:Luft'sDisease Adiseasespecificallyinvolvingmitochondrialenergytransductionwasfirstreportedin 1962.A30yearoldpatientwasdescribedwithgeneralweakness,excessive perspiration,ahighcaloricintakewithoutincreaseinbodyweight,andanexcessively elevatedbasalmetabolicrate(ameasureofoxygenutilization).Itwasdemonstratedthat thepatienthadadefectinthemechanismthatcontrolsmitochondrialoxygenutilization (seeChapter6).TheconditionisreferredtoasLuft'sdisease.Sincethattime,over100 mitochondrialbaseddiseaseshavebeenidentified,includingthoseinvolvingavarietyof enzymesandtransportsystemsrequiredforthepropermaintenanceandcontrolofenergy conservation.Manyinvolveskeletalmuscleandthecentralnervoussystem.Replicationof mitochondriadependsonthemitochondrialDNA(mtDNA)andinheritanceof mitochondriaisbymaternaltransmission.MutationsofmtDNAaswellasnuclearDNA leadtogeneticdiseases.Mitochondrialdamagemayalsooccurduetofreeradical (superoxides)formationwhichcandamagemtDNA.Thusagerelateddegenerative diseases,suchasParkinson'sandAlzheimer's,andcardiomyopathiesmayhavea componentofmitochondrialdamage.FordetailsofspecificdiseasesseeClin.Corr.13.4 and14.6. Luft,R.Thedevelopmentofmitochondrialmedicine.Proc.Natl.Acad.Sci.USA 91:8731,1994. PlasmaMembraneIstheLimitingBoundaryofaCell Theplasmamembraneofeverycellhasauniqueroleinmaintenanceofthatcell'sintegrity.Onesurfaceisincontactwithavariableexternalenvironmentandthe otherwitharelativelyconstantenvironmentprovidedbythecell'scytoplasm.AswillbediscussedinChapter5,thetwosidesoftheplasmamembrane,andall intracellularmembranes,havedifferentchemicalcompositionsandfunctions.Amajorroleoftheplasmamembraneistopermitentranceofsomesubstancesbut excludemanyothers.Withcytoskeletalelements,theplasmamembraneisinvolvedincellshapeandmovements.Throughthismembranecellscommunicatethe membranecontainsmanyspecificreceptorsitesforchemicalsignals,suchashormones(Chapter20),releasedbyothercells.Theinnersurfaceofplasmamembranes isthesiteforattachmentofsomeenzymesinvolvedinvariousmetabolicpathways.Plasmamembranesfromavarietyofcellshavebeenisolatedandstudied extensivelydetailsoftheirstructureandbiochemistryandthoseofothermembranesarepresentedinChapter5. NucleusIsSiteofDNAandRNASynthesis Earlymicroscopistsdividedtheinteriorofcellsintoanucleus,thelargestmembraneboundcompartment,andthecytoplasm.Thenucleusissurroundedbytwo membranes,termedthenuclearenvelope,withtheoutermembranebeingcontinuouswithmembranesoftheendoplasmicreticulum.Thenuclearenvelopehas numerousporesabout90indiameterthatpermitflowofallbutthelargestmoleculesbetweennuclearmatrixandcytoplasm.Thenucleuscontainsa subcompartment,seenclearlyinelectronmicrographs,thenucleolus.Thevastamountofcellulardeoxyribonucleicacid(DNA)islocatedinthenucleusasaDNA proteincomplex,chromatin,thatisorganizedintochromosomes.DNAistherepositoryofgeneticinformationandtheimportanceofthenucleusincelldivisionand forcontrollingphenotypicexpressionofgeneticinformationiswellestablished.BiochemicalreactionsinthenucleusarereplicationofDNAduringmitosis,repairof DNAfollowingdamage(Chapter15),andtranscriptionoftheinformationstoredinDNAintoaformthatcanbetranslatedintocellproteins(Chapter16). TranscriptionofDNAinvolvessynthesisofribonucleicacid(RNA)thatisprocessedintoavarietyofformsfollowingsynthesis.Partofthisprocessingoccursinthe nucleolus,whichisveryrichinRNA. EndoplasmicReticulumHasaRoleinManySyntheticPathways Thecytoplasmofmosteukaryoticcellscontainsanetworkofinterconnectingmembranesthatenclosechannels,cisternae,thatthreadfromtheperinuclearenvelope totheplasmamembrane.Thisextensivesubcellularstructure,termedendoplasmicreticulum,consistsofmembraneswitharoughappearanceinsomeareasand smoothinotherplaces.Theroughappearanceisduetothepresenceofribonucleoproteinparticles,thatis,ribosomes,attachedonthecytosolicsideofthe membrane.Smoothendoplasmicreticulumdoesnotcontainboundribosomes.Duringcellfractionationtheendoplasmicreticulumnetworkisdisrupted,withthe membraneresealingintosmallvesiclescalledmicrosomesthatcanbeisolatedbydifferentialcentrifugation.Microsomespersedonotoccurincells. Amajorfunctionofribosomesonroughendoplasmicreticulumisbiosynthesisofproteinsforexporttotheoutsideofthecellandproteinsforincorporationinto cellularorganellessuchastheendoplasmicreticulum,Golgiapparatus,plasmamembrane,andlysosomes.Smoothendoplasmicreticulumisinvolvedinmembrane lipidsynthesisandcontainsanimportantclass 38. Page17 ofenzymestermedcytochromesP450thatcatalyzehydroxylationofavarietyofendogenousandexogenouscompounds.Theseenzymesareimportantin biosynthesisofsteroidhormonesandremovaloftoxicsubstances(seeChapter23).EndoplasmicreticulumwiththeGolgiapparatushasaroleinformationofother cellularorganellessuchaslysosomesandperoxisomes. TheGolgiApparatusIsInvolvedinSequesteringofProteins TheGolgiapparatusisanetworkofflattenedsmoothmembranesandvesiclesresponsibleforthesecretiontotheexternalenvironmentofavarietyofproteins synthesizedontheendoplasmicreticulum.Golgimembranescatalyzethetransferofcarbohydrateandlipidprecursorstoproteinstoformglycoproteinsand lipoproteinsandisamajorsiteofnewmembraneformation.MembranevesiclesareformedintheGolgiapparatusinwhichvariousproteinsandenzymesare encapsulatedtobesecretedfromthecellafteranappropriatesignal.Digestiveenzymessynthesizedbythepancreasarestoredinintracellularvesiclesformedbythe Golgiapparatusandreleasedwhenneededinthedigestiveprocess(seep.1059).Theroleinmembranesynthesisalsoincludestheformationofintracellularorganelles suchaslysosomesandperoxisomes. TABLE1.7RepresentativeLysosomalEnzymesandTheir Substrates TypeofSubstrateandEnzyme SpecificSubstrate POLYSACCHARIDE HYDROLYZING ENZYMES aGlucosidase Glycogen aFlucosidase Membranefucose Galactosides bGalactosidase Mannosides aMannosidase Glucuronides bGlucuronidase Hyaluronidase Hyaluronicacidand chondroitinsulfates Arylsulfatase Organicsulfates Lysozyme Bacterialcellwalls PROTEINHYDROLYZING ENZYMES Cathepsins Proteins Collagenase Collagen Elastase Elastin Peptidases Peptides NUCLEICACID HYDROLYZING ENZYMES Ribonuclease RNA Deoxyribonuclease DNA LIPIDHYDROLYZING ENZYMES Lipases Triglycerideand cholesterolesters Esterase Fattyacidesters Phospholipase Phospholipids PHOSPHATASES Phosphatase Phospho monoesters Phosphodiesterase Phosphodiesters SULFATASES Heparansulfate Dermatansulfate MitochondriaSupplyMostCellNeedsforATP Mitochondriaappearasspheres,rods,orfilamentousbodiesthatareusuallyabout0.51mmindiameterandupto7mminlength.Theinternalmatrix,themitosol, issurroundedbytwomembranes,distinctivelydifferentinappearanceandbiochemicalfunction.Theinnermembraneconvolutesintothematrixtoformcristaeand containsnumeroussmallspheresattachedbystalksontheinnersurface.Outerandinnermembranescontaindifferentenzymes.Thecomponentsoftherespiratory chainandthemechanismforATPsynthesisarepartoftheinnermembraneandaredescribedindetailinChapter6.Majormetabolicpathwaysinvolvedinoxidation ofcarbohydrates,lipids,andaminoacids,andpartsofspecialbiosyntheticpathwaysinvolvingureaandhemesynthesisarelocatedinthemitosol.Theoutermembrane isrelativelypermeablebuttheinnermembraneishighlyselectiveandcontainsavarietyoftransmembranetransportsystems. MitochondriacontainaspecificDNA,withgeneticinformationforsomeofthemitochondrialproteins,andthebiochemicalequipmentforlimitedproteinsynthesis.The presenceofthisbiosyntheticcapacityindicatestheuniquerolethatmitochondriahaveintheirowndestiny.SeeClin.Corr.1.2fordescriptionsofdiseasesattributedto deficitsinmitochondrialfunction. LysosomesAreRequiredforIntracellularDigestion Intracellulardigestionofavarietyofsubstancesoccursinsidestructuresdesignatedaslysosomes.TheyhaveasinglelimitingmembraneandmaintainapHlowerin thelysosomalmatrixthanthatofthecytosol.Encapsulatedinlysosomesisagroupofglycoproteinenzymeshydrolasesthatcatalyzehydrolyticcleavageofcarbon oxygen,carbonnitrogen,carbonsulfur,andoxygenphosphorusbondsinproteins,lipids,carbohydrates,andnucleicacids.Apartiallistoflysosomalenzymesis presentedinTable1.7.Asingastrointestinaldigestion,lysosomalenzymessplitcomplexmoleculesintosimplelowmolecularweightcompoundsthatcanbeutilizedby metabolicpathwaysofthecell.EnzymesofthelysosomearecharacterizedbybeingmostactivewhenthepHofthemediumisacidic,thatis,pH5andbelow.The relationshipbetweenpHandenzymeactivityisdiscussedinChapter4.ThepHofthecytosolisclosetopH7.0andlysosomalenzymeshavelittleactivityatthispH. 39. Page18 CLINICALCORRELATION1.3 LysosomalEnzymesandGout Catabolismofpurines,nitrogencontainingheterocycliccompoundsfoundinnucleic acids,leadstoformationofuricacid,whichisexcretedintheurine(seeChapter12for details).Goutisanabnormalityinwhichthereisexcessiveuricacidproductionwithan increaseinuricacidinbloodanddepositionofuratecrystalsinjoints.Theconsequences areclinicalmanifestationsinthejoint,particularlythebigtoe,includinginflamma